@article {pmid38054624, year = {2023}, author = {Satheesh Babu, AK and Petersen, C and Paz, HA and Iglesias-Carres, L and Li, Y and Zhong, Y and Neilson, AP and Wankhade, UD and Anandh Babu, PV}, title = {Gut Microbiota Depletion Using Antibiotics to Investigate Diet-Derived Microbial Metabolites: An Efficient Strategy.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e2300386}, doi = {10.1002/mnfr.202300386}, pmid = {38054624}, issn = {1613-4133}, support = {R01AT010247/AT/NCCIH NIH HHS/United States ; }, abstract = {SCOPE: Gut microbiota depletion using antibiotics in drinking water is a valuable tool to investigate the role of gut microbes and microbial metabolites in health and disease. However, there are challenges associated with this model. Animals avoid drinking water because of the antibiotic bitterness, which affects their metabolic health. The present study develops an efficient strategy to deplete gut microbes without affecting metabolic parameters.<br><br>METHODS AND RESULTS: Male C57BL/6J mice (7 weeks old) are fed a control (C) or high-fat (HF) diet. Subgroups of C and HF mice receive an antibiotic cocktail in drinking water (CA and HA). The antibiotic dosage is gradually increased so that the animals adapt to the taste of antibiotics. Metabolic parameters, gut microbiome, and microbial metabolites are assessed after 12 weeks treatment. Culture methods and 16s rRNA amplification confirm the depletion of gut microbes in antibiotic groups (CA and HA). Further, antibiotic treatment does not alter metabolic parameters (body weight, body fat, lean body mass, blood glucose, and glucose/insulin tolerance), whereas it suppresses the production of diet-derived microbial metabolites (trimethylamine and trimethylamine-N-oxide).<br><br>CONCLUSION: This strategy effectively depletes gut microbes and suppresses the production of microbial metabolites in mice without affecting their metabolic health.}, }
@article {pmid38054580, year = {2023}, author = {Kim, S and Jung, Y and Lee, SB and Oh, HS and Hong, SN}, title = {Gut microbial signatures in clinically stable ulcerative colitis according to the mucosal state and associated symptoms.}, journal = {Journal of gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jgh.16434}, pmid = {38054580}, issn = {1440-1746}, support = {UUH-2021-10//Ulsan University Hospital Research Center/ ; }, abstract = {BACKGROUND AND AIM: The gut microbiome of patients with clinically stable ulcerative colitis (UC) differs from that of healthy individuals depending on the state of the colonic mucosa, especially with or without advanced scarring; however, the underlying mechanism is unclear. Therefore, this study examined the gut microbiome compositional signatures in patients with significant mucosal scarring and UC-related symptoms.<br><br>METHODS: Stool samples for gut microbiome analysis were prospectively collected from 57 patients with clinically stable UC between January 1 and December 31, 2022. Data from 57 individuals without inflammatory bowel disease (non-IBD) paired by age and sex were selected from our previous study as the control group. The fecal samples were subjected to 16S rRNA gene sequencing. Associations between gut microbiome profiles and clinical or colonoscopic assessments were examined using diversity and differential abundance analyses.<br><br>RESULTS: Gut microbiome compositions between the patients with clinically stable UC and non-IBD controls differed significantly. Furthermore, gut microbiome compositions varied between the preserved and altered mucosa groups identified based on mucosal changes in the UC group. Differential abundance test of patients with UC for symptomatic remission based on stool frequency from the two-item patient-reported outcome identified several overlapping taxa specified as gut microbiome signatures, including the Enterobacteriaceae unknown genera (Enterobacteriaceae_g), Klebsiella,&#xa0;and several Lachnospiraceae spp. both in mucosal and symptom change analyses.<br><br>CONCLUSIONS: The gut microbiome can change with mucosal changes, even in clinically stable UC, and some gut microbial signatures may explain the symptom manifestations in patients with UC showing significant mucosal changes.}, }
@article {pmid38054020, year = {2023}, author = {Du, L and Dong, X and Song, J and Lei, T and Liu, X and Lan, Y and Liu, X and Wang, J and Yue, B and He, M and Fan, Z and Guo, T}, title = {Temporal and spatial differences in the vaginal microbiome of Chinese healthy women.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16438}, pmid = {38054020}, issn = {2167-8359}, mesh = {Female ; Humans ; *East Asian People ; Vagina/microbiology ; Lactobacillus ; Cervix Uteri/microbiology ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Up the reproductive tract, there are large differences in the composition of vaginal microbes. Throughout the menstrual cycle, the structure of the vaginal microbiome shifts. Few studies have examined both in combination. Our study was designed to explore trends in the microbiome of different parts of the vagina in healthy women over the menstrual cycle.<br><br>METHODS: We performed metagenomic sequencing to characterize the microbiome differences between the cervical orifice and mid-vagina throughout the menstrual cycle.<br><br>RESULTS: Our results showed the vaginal microbiome of healthy women in the cervical orifice and the mid-vagina was similar during the periovulatory and luteal phases, with Lactobacillus being the dominant bacteria. In the follicular phase, Acinetobacter was detected in the cervical orifice. From the follicular phase to the luteal phase, the community state types (all five community status types were defined as CSTs) in samples No. 10 and No. 11 changed from CST III to CST I. In addition, the composition of the vaginal microbiome in healthy women from different regions of China was significantly different. We also detected viruses including Human alphaherpesvirus 1 (HSV-1) during periovulatory phase.<br><br>CONCLUSION: This study is valuable for understanding whether the microbial composition of the vagina is consistent in different parts of the menstrual cycle.}, }
@article {pmid38053996, year = {2023}, author = {Wang, ZY and Zheng, YX and Xu, F and Cui, YZ and Chen, XY and Chen, SQ and Yan, BX and Zhou, Y and Zheng, M and Man, XY}, title = {Epidermal keratinocyte-specific STAT3 deficiency aggravated atopic dermatitis-like skin inflammation in mice through TSLP upregulation.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1273182}, pmid = {38053996}, issn = {1664-3224}, mesh = {Animals ; Mice ; *Dermatitis, Atopic/chemically induced/genetics ; Thymic Stromal Lymphopoietin ; Up-Regulation ; STAT3 Transcription Factor/genetics/metabolism ; Dinitrochlorobenzene ; Cytokines/metabolism ; Keratinocytes ; Inflammation/metabolism ; }, abstract = {Atopic dermatitis (AD) is one of the most common inflammatory skin diseases with complex pathogenesis involving epidermal barrier dysfunction, skin microbiome abnormalities and type-2-skewed immune dysregulation. Signal transducer and activator of transcription 3 (STAT3) is a transcription factor that plays critical roles in various biological processes. However, the role of STAT3 in epidermal keratinocytes in AD remains unclear. In this study, we generated an epidermal keratinocyte-specific Stat3-deficient mouse strain (termed Stat3 cKO mice). After topical 2,4-dinitrochlorobenzene (DNCB) treatment, Stat3 cKO mice developed worsened AD-like skin inflammation with increased Ki67[+] cells, decreased filaggrin and loricrin expression, and downregulated S100A9 and LL37. The dominant microbial population in Stat3 cKO mice changed from Ralstonia to Staphylococcus. DNCB-treated Stat3 cKO mice displayed more infiltrating type-2 inflammatory cells, including mast cells, eosinophils, and CD4[+]T cells, accompanied by increased skin IL-4 and serum IgE levels. Moreover, thymic stromal lymphopoietin (TSLP), mainly produced by keratinocytes, was highly expressed in the ear skin of Stat3 cKO mice and chemoattracted more TSLPR[+] cells. TSLP blockade significantly alleviated DNCB-induced AD-like skin inflammation in Stat3 cKO mice. Thus, epidermal keratinocyte-specific STAT3 deficiency can aggravate AD-like skin inflammation in mice, possibly through TSLP dysregulation.}, }
@article {pmid38053902, year = {2023}, author = {Maust, BS and Petkov, S and Herrera, C and Feng, C and Brown, BP and Lebina, L and Opoka, D and Ssemata, A and Pillay, N and Serwanga, J and Seatlholo, P and Namubiru, P and Odoch, G and Mugaba, S and Seiphetlo, T and Gray, CM and Kaleebu, P and Webb, EL and Martinson, N and Chiodi, F and Fox, J and Jaspan, HB and , }, title = {Bacterial microbiome and host inflammatory gene expression in foreskin tissue.}, journal = {Heliyon}, volume = {9}, number = {11}, pages = {e22145}, pmid = {38053902}, issn = {2405-8440}, abstract = {The penile epithelial microbiome remains underexplored. We sequenced human RNA and a segment of the bacterial 16S rRNA gene from the foreskin tissue of 144 adolescents from South Africa and Uganda collected during penile circumcision after receipt of 1-2 doses of placebo, emtricitabine + tenofovir disoproxil fumarate, or emtricitabine + tenofovir alafenamide to investigate the microbiome of foreskin tissue and its potential changes with antiretroviral use. We identified a large number of anaerobic species, including Corynebacterium acnes, which was detected more frequently in participants from South Africa than Uganda. Bacterial populations did not differ by treatment received, and no differentially abundant taxa were identified between placebo versus active drug recipients. The relative abundance of specific bacterial taxa was negatively correlated with expression of genes downstream of the innate immune response to bacteria and regulation of inflammation. Our results show no difference in the tissue microbiome of the foreskin with short-course antiretroviral use but that bacterial taxa were largely inversely correlated with inflammatory gene expression, consistent with commensal colonization.}, }
@article {pmid38053882, year = {2023}, author = {Dai, W and Liu, Y and Zhang, X and Dai, L}, title = {16S rDNA profiling of Loach (Misgurnus anguillicus) fed with soybean fermented powder intestinal flora in response to Lipopolysaccharide (LPS) infection.}, journal = {Heliyon}, volume = {9}, number = {11}, pages = {e22369}, pmid = {38053882}, issn = {2405-8440}, abstract = {Soybean fermentation has a balancing effect on the regulation of intestinal flora. Relative research between fermented soybeans and intestinal microbiota is limited. Our aim was to explore the effects of soybean fermented fowder on lipopolysaccharide (LPS) induced intestinal microflora and corresponding functions in loach. 16S rDNA high-throughout sequencing was applied to estimate differences in the intestinal microbiota and predict genes function. Analysis of the overall of sequencing data showed that the ratio of Effective Tags in both the control group and the treatment group was greater than 80 %. Based on six major classifications involved in the phylum, class, order, family, genus, and species, we acquired the changes in the composition of intestinal microorganisms after the supplement of soybean fermented powder. These results showed that the dominant bacteria in the two groups were basically distinct at different levels. Alpha diversity analysis indicated that the microbial richness and uniformity of soybean fermented powder decreased compared to the control group. PICRUSt and Taxfun tools analysis of intestinal flora illustrated the functional genes of the six groups were mainly involved in metabolism, genetic information processing, cellular processes, environmental information processing, and human diseases at the level 1. These data clearly demonstrated the effect of soybean fermented powder on the gut microbiome. Not only that, it provides new ideas and insights for achieving high-quality utilization of soybean fermented powder. The potential mechanisms of soybean fermented powder to alter gut flora and intestinal microbiome function can further be explored.}, }
@article {pmid38053859, year = {2023}, author = {Sharma, S and Bakht, A and Jahanzaib, M and Kim, M and Lee, H and Park, C and Park, D}, title = {Characterization of bacterial species and antibiotic resistance observed in Seoul, South Korea's popular Gangnam-gu area.}, journal = {Heliyon}, volume = {9}, number = {11}, pages = {e21751}, pmid = {38053859}, issn = {2405-8440}, abstract = {Public transportation facilities, especially road crossings, which raise the pathogenic potential of urban environments, are the most conducive places for the transfer of germs between people and the environment. It is necessary to study the variety of the microbiome and describe its unique characteristics to comprehend these relationships. In this investigation, we used 16 S rRNA gene sample sequencing to examine the biological constituents and inhalable, thoracic, and alveolar particles in aerosol samples collected from busy areas in the Gangnam-gu district of the Seoul metropolitan area using a mobile vehicle. We also conducted a comparison analysis of these findings with the previously published data and tested for antibiotic resistance to determine the distribution of bacteria related to the human microbiome and the environment. Actinobacteria, Cyanobacteria, Bacteriodetes, Proteobacteria, and Firmicutes were the top five phyla in the bacterial 16 S rRNA libraries, accounting for >90 % of all readings across all examined locations. The most prevalent classes among the 12 found bacterial classes were Bacilli (45.812 %), Gammaproteobacteria (25.238 %), Tissierellia (13.078 %), Clostridia (5.697 %), and Alphaproteobacteria (5.142 %). The data acquired offer useful information on the variety of bacterial communities and their resistance to antibiotic drugs on the streets of Gangnam-gu, one of the most significant social centers in the Seoul metropolitan area. This work emphasizes the relevance of biological particles and particulate matter in the air, and it suggests more research is needed to perform biological characterization of the ambient particulate matter.}, }
@article {pmid38053837, year = {2023}, author = {Xia, W and Li, S and Li, L and Zhang, S and Wang, X and Ding, W and Ding, L and Zhang, X and Wang, Z}, title = {Role of anthraquinones in combating insulin resistance.}, journal = {Frontiers in pharmacology}, volume = {14}, number = {}, pages = {1275430}, pmid = {38053837}, issn = {1663-9812}, abstract = {Insulin resistance presents a formidable public health challenge that is intricately linked to the onset and progression of various chronic ailments, including diabetes, cardiovascular disease, hypertension, metabolic syndrome, nonalcoholic fatty liver disease, and cancer. Effectively addressing insulin resistance is paramount in preventing and managing these metabolic disorders. Natural herbal remedies show promise in combating insulin resistance, with anthraquinone extracts garnering attention for their role in enhancing insulin sensitivity and treating diabetes. Anthraquinones are believed to ameliorate insulin resistance through diverse pathways, encompassing activation of the AMP-activated protein kinase (AMPK) signaling pathway, restoration of insulin signal transduction, attenuation of inflammatory pathways, and modulation of gut microbiota. This comprehensive review aims to consolidate the potential anthraquinone compounds that exert beneficial effects on insulin resistance, elucidating the underlying mechanisms responsible for their therapeutic impact. The evidence discussed in this review points toward the potential utilization of anthraquinones as a promising therapeutic strategy to combat insulin resistance and its associated metabolic diseases.}, }
@article {pmid38053727, year = {2023}, author = {Ma, L and La, X and Zhang, B and Xu, W and Tian, C and Fu, Q and Wang, M and Wu, C and Chen, Z and Chang, H and Li, JA}, title = {Total Astragalus saponins can reverse type 2 diabetes mellitus-related intestinal dysbiosis and hepatic insulin resistance in vivo.}, journal = {Frontiers in endocrinology}, volume = {14}, number = {}, pages = {1190827}, pmid = {38053727}, issn = {1664-2392}, mesh = {Rats ; Male ; Animals ; *Diabetes Mellitus, Type 2/complications/drug therapy ; *Insulin Resistance ; Blood Glucose/metabolism ; Glycogen Synthase Kinase 3 beta/metabolism/pharmacology ; *Saponins/pharmacology/metabolism ; Dysbiosis/drug therapy ; Rats, Sprague-Dawley ; *Diabetes Mellitus, Experimental/complications/drug therapy ; Liver/metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; RNA, Messenger/metabolism ; Cholesterol/metabolism ; }, abstract = {OBJECTIVE: Intestinal flora homeostasis in rats with type 2 diabetes mellitus (T2DM) was evaluated to explore the effects of total Astragalus saponins (TAS) on hepatic insulin resistance (IR).<br><br>METHODS: Six-week-old male Sprague-Dawley rats were fed high-fat and high-sugar diet for 4 weeks and intraperitoneally injected with streptozotocin to induce T2DM, and they were then randomly divided into control, model, metformin, and TAS groups. Stool, serum, colon, and liver samples were collected after 8 weeks of drug administration for relevant analyses.<br><br>RESULTS: TAS reduced fasting blood glucose, 2-hour postprandial blood glucose, area under the curve of oral glucose tolerance test, glycated serum protein, homeostasis model assessment of insulin resistance, total cholesterol, triglyceride, and low-density lipoprotein cholesterol levels in T2DM rats but increased insulin, C-peptide, and high-density lipoprotein cholesterol levels. Moreover, TAS improved the morphology and structure of liver and colon tissues and improved the composition of the intestinal microbiome and bacterial community structure at different taxonomic levels. In addition, TAS increased the protein expression of hepatic IRS-1, PI3K, PDK1, and p-AKT and decreased the protein expression of p-GSK-3&#x3b2;. Meanwhile, TAS increased the mRNA expression of liver PDK1, PI3K, and GS and decreased the mRNA expression of GSK-3&#x3b2;.<br><br>CONCLUSION: TAS can ameliorate T2DM-related abnormal glucose and blood lipid metabolism, intestinal dysbiosis, and IR.}, }
@article {pmid38053586, year = {2023}, author = {Lawrence, P and Padamsee, M and Lee, K and Lacap-Bugler, DC}, title = {Soil microbial functional gene dataset associated with Agathis australis.}, journal = {Data in brief}, volume = {51}, number = {}, pages = {109791}, pmid = {38053586}, issn = {2352-3409}, abstract = {Agathis australis (New Zealand kauri) is a significant and iconic native tree of Aotearoa New Zealand. Currently, Phytophthora agathidicida that causes kauri-dieback disease is killing kauri trees. Only 1% of the New Zealand virgin kauri forest remains [1,2]. Recent studies revealed that many soil-borne microorganisms had been found to systemically boost the defensive capacity of the trees by providing competition to pathogens for nutrient intake, thus preventing pathogen colonization and modulating plant immunity [3,4]. In addition, the root microbiome consists of an entire complex rhizosphere-associated microbes with their genetic elements and interactions that have influenced plant health. To date, very few studies have been conducted to investigate the microorganisms in the kauri soil and possible environmental drivers. To characterize the functional gene profile in relation to soil microbial diversity of the kauri trees at Auckland Botanic Gardens (ABG), Auckland, New Zealand the GeoChip 5.0 M (Glomics Inc. USA), a microarray-based metagenomics tool, was used. GeoChip 5.0 M comprises of 162,000 probes from 365,000 target genes (coding DNA sequence - CDS), which covers all taxonomic groups (archaea, bacteria, fungi, protists, algae, and viruses) [5]. The ABG has kauri trees that are approximately 20 years old, located in three distinct man-made environments: Native Forest, Kauri Grove, and Rose Garden. We selected two trees from the Native Forest and two from the Kauri Grove for our experiment. Soil samples were collected from the four cardinal points of each tree, at 10 cm depth. Pooled environmental DNA was sent to Glomics (USA) and the data were preprocessed using GeoChip data analysis pipeline described in http://www.ou.edu/ieg/tools/data-analysispipeline.html. Based on the GeoChip data generated from the soil samples, we have detected a total of 946 genes, 4342 taxa, 102 phyla, and 995 genera. The data presented here provide an overview of functional genes associated with kauri soil, which can serve as baseline for other kauri soil microbiome analysis at forest-scale studies. The raw data has been uploaded to Mendeley Data https://doi.org/10.17632/T22NNN385K.1.}, }
@article {pmid38053580, year = {2023}, author = {Zuo, Z and Pei, L and Liu, T and Liu, X and Chen, Y and Hu, Z}, title = {Investigation of Gut Microbiota Disorders in Sepsis and Sepsis Complicated with Acute Gastrointestinal Injury Based on 16S rRNA Genes Illumina Sequencing.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {7389-7403}, pmid = {38053580}, issn = {1178-6973}, abstract = {BACKGROUND: Sepsis is a life-threatening organ dysfunction caused by the host's dysfunctional response to infection, which can cause acute gastrointestinal injury (AGI). The gut microbiota is dynamic and plays a role in the immune and metabolic. The aim of this study was to investigate the composition and function of gut microbiota in patients with sepsis, as well as the gut microbiome that may be involved in the occurrence of AGI.<br><br>METHODS: A total of 23 stool samples from healthy control individuals and 41 stool samples from sepsis patients were collected. Patients with sepsis were followed up for one week to observe whether AGI has occurred. Finally, 41 patients included 21 sepsis complicated with AGI (referred to as Com-AGI) and 20 sepsis without complicated with AGI (referred to as No-AGI). The gut microbiota was analyzed by 16S rRNA gene sequencing, followed by composition analysis, difference analysis, correlation analysis, functional prediction analysis.<br><br>RESULTS: The diversity and evenness of gut microbiota were decreased in patients with sepsis. Compared with No-AGI, the gut microbiota of Com-AGI has higher community diversity, richness, and phylogenetic diversity. Escherichia-Shigella, Blautia and Enterococcus may be important indicators of sepsis. The correlation analysis showed that aspartate aminotransferase (AST) and Barnesiella have the most significant positive correlation. Moreover, Clostridium_innocuum_group, Christensenellaceae_R-7_group and Eubacterium were all significantly correlated with LAC and DAO. Clostridium_innocuum_group, Barnesiella, Christensenellaceae_R-7_group and Eubacterium may play important roles in the occurrence of AGI in sepsis. PICRUSt analysis revealed multiple functional pathways involved in the relationship between gut microbiota and sepsis, including starch degradation V, glycogen degradation I (bacterial), Lipoic acid metabolism and Valine, leucine and isoleucine biosynthesis. BugBase analysis showed that the gut microbiota with Aerobic phenotype may play an important role in sepsis.<br><br>CONCLUSION: Dysfunction of gut microbiota was associated with sepsis and AGI in patients with sepsis.}, }
@article {pmid38053550, year = {2023}, author = {Jiang, X and Deng, S and Lu, N and Yao, W and Xia, D and Tu, W and Lei, H and Jia, P and Gan, Y}, title = {Fecal microbial composition associated with testosterone in the development of Meishan male pigs.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1257295}, pmid = {38053550}, issn = {1664-302X}, abstract = {INTRODUCTION: The gut microbiota closely relates to host health, whereas the relationship between gut microbiota and testosterone during the development of Meishan male pigs remains unclear. This study investigated the fecal microbiota composition and testosterone level during development in Meishan male pigs.<br><br>METHODS: Fresh fecal samples of 20 healthy Meishan male pigs were individually collected at 10 and 22 weeks (wk) of age for testosterone content detection and bacteria pyrosequencing analysis. Anaerobic culture experiment of fecal bacteria in vitro was performed for bacteria pyrosequencing analysis.<br><br>RESULTS: The fecal testosterone content increased significantly from 10 weeks (wk) to 22 wk of age (P < 0.05). Meanwhile, the boars at 22 wk had a lower abundance of phylum Bacteroidetes and Proteobacteria, and genus Alloprevotella, Prevotella_1, Prevotellaceae_NK3B31_group, and Streptococcus in the fecal microbiota composition (P < 0.05). but higher proportions of the phylum Actinobacteria, Firmicutes, Kiritimatiellaeota, and Tenericutes, and genus Clostridium_sensu_stricto_1, Muribaculaceae and Terrisporobacter than that at 10 wk (P < 0.05), and the Firmicutes to Bacteroidetes ratio was higher at 22 wk than 10 wk (P < 0.05). Moreover, the fecal testosterone level significantly correlated with the relative abundance of the phylum Actinobacteria, Firmicutes, and Tencuteseri, and genus Alloprevotella, Clostridium_sensu_stricto_1, Muribaculaceae, Prevotella_1 and Streptococcus. Furthermore, the in vitro experiments indicated that the abundance of the phylum Proteobacteria and genus Escherichia-Shigella reduced with the increase of supplemental testosterone level. In contrast, the proportion of Firmicutes phylum increased with additional testosterone levels.<br><br>DISCUSSION: Testosterone could modulate the microflora structure. Meanwhile, the bacteria could degrade the testosterone in a dose testosterone-dependent manner. These results provide us with new insights into the relationship between the gut microbiome and testosterone and the contributions of the gut microbiome in physiological regulation in response to gonad development.}, }
@article {pmid38053532, year = {2023}, author = {Zhou, YM and Yuan, JJ and Xu, YQ and Gou, YH and Zhu, YYX and Chen, C and Huang, XX and Ma, XM and Pi, M and Yang, ZX}, title = {Fecal microbiota as a predictor of acupuncture responses in patients with postpartum depressive disorder.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1228940}, pmid = {38053532}, issn = {2235-2988}, mesh = {Female ; Humans ; Treatment Outcome ; *Acupuncture Therapy ; *Microbiota ; *Depressive Disorder/therapy ; Biomarkers ; Postpartum Period ; }, abstract = {BACKGROUND: There are several clinical and molecular predictors of responses to antidepressant therapy. However, these markers are either too subjective or complex for clinical use. The gut microbiota could provide an easily accessible set of biomarkers to predict therapeutic efficacy, but its value in predicting therapy responses to acupuncture in patients with depression is unknown. Here we analyzed the predictive value of the gut microbiota in patients with postpartum depressive disorder (PPD) treated with acupuncture.<br><br>METHODS: Seventy-nine PPD patients were enrolled: 55 were treated with acupuncture and 24 did not received any treatment. The 17-item Hamilton depression rating scale (HAMD-17) was used to assess patients at baseline and after eight weeks. Patients receiving acupuncture treatment were divided into an acupuncture-responsive group or non-responsive group according to HAMD-17 scores changes. Baseline fecal samples were obtained from the patients receiving acupuncture and were analyzed by high-throughput 16S ribosomal RNA sequencing to characterize the gut microbiome.<br><br>RESULTS: 47.27% patients responded to acupuncture treatment and 12.5% patients with no treatment recovered after 8-week follow-up. There was no significant difference in &#x3b1;-diversity between responders and non-responders. The &#x3b2;-diversity of non-responders was significantly higher than responders. Paraprevotella and Desulfovibrio spp. were significantly enriched in acupuncture responders, and these organisms had an area under the curve of 0.76 and 0.66 for predicting responder patients, respectively.<br><br>CONCLUSIONS: Paraprevotella and Desulfovibrioare may be useful predictive biomarkers to predict PPD patients likely to respond to acupuncture. Larger studies and validation in independent cohorts are now needed to validate our findings.}, }
@article {pmid38053528, year = {2023}, author = {Hammad, MI and Conrads, G and Abdelbary, MMH}, title = {Isolation, identification, and significance of salivary Veillonella spp., Prevotella spp., and Prevotella salivae in patients with inflammatory bowel disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1278582}, pmid = {38053528}, issn = {2235-2988}, mesh = {Humans ; *Veillonella/genetics ; RNA, Ribosomal, 16S/genetics ; Vancomycin ; Agar ; Bacteria ; Prevotella/genetics ; *Inflammatory Bowel Diseases ; }, abstract = {The global prevalence of inflammatory bowel disease (IBD) is on the rise, prompting significant attention from researchers worldwide. IBD entails chronic inflammatory disorders of the intestinal tract, characterized by alternating flares and remissions. Through high-throughput sequencing, numerous studies have unveiled a potential microbial signature for IBD patients showing intestinal enrichment of oral-associated bacteria. Simultaneously, the oral microbiome can be perturbed by intestinal inflammation. Our prior investigation, based on 16S rRNA amplicon sequencing, underscored elevated abundance of Veillonella spp. and Prevotella spp. in the salivary microbiomes of IBD patients. Noteworthy, Prevotella salivae emerged as a distinct species significantly associated with IBD. P. salivae is an under-recognized pathogen that was found to play a role in both oral and systemic diseases. In this study, we delve deeper into the salivary microbiomes of both IBD patients and healthy controls. Employing diverse cultivation techniques and real-time quantitative polymerase chain reactions (RT-qPCR), we gauged the prevalence and abundance of Veillonella spp., Prevotella spp., and P. salivae. Our isolation efforts yielded 407 and 168 strains of Veillonella spp., as well as 173 and 90 strains of Prevotella spp., from the saliva samples of IBD patients and healthy controls, respectively. Veillonella-vancomycin agar emerged as the discerning choice for optimal Veillonella spp. cultivation, while Schaedler kanamycin-vancomycin agar proved to be the most suitable medium for cultivating Prevotella spp. strains. Comparing our RT-qPCR findings to the previous 16S rRNA amplicon sequencing data, the results corroborated the higher abundance of Veillonella spp., Prevotella spp., and P. salivae in the saliva of IBD patients compared to healthy controls. However, it's worth noting that in contrast to RT-qPCR, the 16S rRNA amplicon sequencing data revealed greater absolute abundance of all three bacterial groups in both IBD patients and controls.}, }
@article {pmid38053218, year = {2023}, author = {Prioux, C and Tignat-Perrier, R and Gervais, O and Estaque, T and Schull, Q and Reynaud, S and Béraud, E and Mérigot, B and Beauvieux, A and Marcus, MI and Richaume, J and Bianchimani, O and Cheminée, A and Allemand, D and Ferrier-Pagès, C}, title = {Unveiling microbiome changes in Mediterranean octocorals during the 2022 marine heatwaves: quantifying key bacterial symbionts and potential pathogens.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {271}, pmid = {38053218}, issn = {2049-2618}, mesh = {Animals ; Bacteria/genetics ; *Anthozoa/microbiology ; *Microbiota ; Temperature ; Forests ; Coral Reefs ; }, abstract = {BACKGROUND: Climate change has accelerated the occurrence and severity of heatwaves in the Mediterranean Sea and poses a significant threat to the octocoral species that form the foundation of marine animal forests (MAFs). As coral health intricately relies on the symbiotic relationships established between corals and microbial communities, our goal was to gain a deeper understanding of the role of bacteria in the observed tissue loss of key octocoral species following the unprecedented heatwaves in 2022.<br><br>RESULTS: Using amplicon sequencing and taxon-specific qPCR analyses, we unexpectedly found that the absolute abundance of the major bacterial symbionts, Spirochaetaceae (C. rubrum) and Endozoicomonas (P. clavata), remained, in most cases, unchanged between colonies with 0% and 90% tissue loss. These results suggest that the impairment of coral health was not due to the loss of the main bacterial symbionts. However, we observed a significant increase in the total abundance of bacterial opportunists, including putative pathogens such as Vibrio, which was not evident when only their relative abundance was considered. In addition, there was no clear relation between bacterial symbiont loss and the intensity of thermal stress, suggesting that factors other than temperature may have influenced the differential response of octocoral microbiomes at different sampling sites.<br><br>CONCLUSIONS: Our results indicate that tissue loss in octocorals is not directly caused by the decline of the main bacterial symbionts but by the proliferation of opportunistic and pathogenic bacteria. Our findings thus underscore the significance of considering both relative and absolute quantification approaches when evaluating the impact of stressors on coral microbiome as the relative quantification does not accurately depict the actual changes in the microbiome. Consequently, this research enhances our comprehension of the intricate interplay between host organisms, their microbiomes, and environmental stressors, while offering valuable insights into the ecological implications of heatwaves on marine animal forests. Video Abstract.}, }
@article {pmid38053159, year = {2023}, author = {Costa, LSAS and de Faria, MR and Chiaramonte, JB and Mendes, LW and Sepo, E and de Hollander, M and Fernandes, JMC and Carrión, VJ and Bettiol, W and Mauchline, TH and Raaijmakers, JM and Mendes, R}, title = {Repeated exposure of wheat to the fungal root pathogen Bipolaris sorokiniana modulates rhizosphere microbiome assembly and disease suppressiveness.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {85}, pmid = {38053159}, issn = {2524-6372}, support = {BB/N016246/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/X010953/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {BACKGROUND: Disease suppressiveness of soils to fungal root pathogens is typically induced in the field by repeated infections of the host plant and concomitant changes in the taxonomic composition and functional traits of the rhizosphere microbiome. Here, we studied this remarkable phenomenon for Bipolaris sorokiniana in two wheat cultivars differing in resistance to this fungal root pathogen.<br><br>RESULTS: The results showed that repeated exposure of the susceptible wheat cultivar to the pathogen led to a significant reduction in disease severity after five successive growth cycles. Surprisingly, the resistant wheat cultivar, initially included as a control, showed the opposite pattern with an increase in disease severity after repeated pathogen exposure. Amplicon analyses revealed that the bacterial families Chitinophagaceae, Anaerolineaceae and Nitrosomonadaceae were associated with disease suppressiveness in the susceptible wheat cultivar; disease suppressiveness in the resistant wheat cultivar was also associated with Chitinophagaceae and a higher abundance of Comamonadaceae. Metagenome analysis led to the selection of 604 Biosynthetic Gene Clusters (BGCs), out of a total of 2,571 identified by AntiSMASH analysis, that were overrepresented when the soil entered the disease suppressive state. These BGCs are involved in the biosynthesis of terpenes, non-ribosomal peptides, polyketides, aryl polyenes and post-translationally modified peptides.<br><br>CONCLUSION: Combining taxonomic and functional profiling we identified key changes in the rhizosphere microbiome during disease suppression. This illustrates how the host plant relies on the rhizosphere microbiome as the first line of defense to fight soil-borne pathogens. Microbial taxa and functions identified here can be used in novel strategies to control soil-borne fungal pathogens.}, }
@article {pmid38053016, year = {2023}, author = {Wang, J and Wu, S and Zhang, J and Li, Y and Wu, Y and Qi, X}, title = {Correlation between gut microbiome and cognitive impairment in patients undergoing peritoneal dialysis.}, journal = {BMC nephrology}, volume = {24}, number = {1}, pages = {360}, pmid = {38053016}, issn = {1471-2369}, support = {1908085MH245//the Natural Science Foundation of Anhui Province/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Cognitive Dysfunction/diagnosis/etiology ; *Kidney Failure, Chronic/complications/therapy ; *Peritoneal Dialysis/adverse effects ; Cognition ; }, abstract = {BACKGROUND: Growing evidence has demonstrated that patients undergoing peritoneal dialysis (PD) are more likely to experience cognitive impairment than patients with non-dialysis end-stage renal disease (ESRD); however, the underlying mechanisms remain unclear. This study aimed to identify the role and predictive significance of gut microbiome alterations in PD-associated cognitive impairment.<br><br>METHODS: A total of 29 non-dialysis ESRD patients and 28 PD patients were enrolled in this study and divided into subgroups according to the Montreal Cognitive Assessment (MoCA). Faecal samples were analyzed using 16&#xa0;S rRNA. Mini-Mental State Examination (MMSE) and MoCA scores were used to assess the degree of cognitive impairment in patients.<br><br>RESULTS: The 16&#xa0;S rRNA analysis demonstrated differences in gut microbiome abundance and structure between PD and non-dialysis ESRD patients and between PD patients with cognitive impairment (PCI) and PD patients with normal cognition (PNCI). At family and genus levels, Prevotellaceae exhibited the greatest structure difference, while Lactobacillus exhibited the greatest abundance difference between PCI and PNCI. Altered microbiota abundance significantly correlated with cognitive function and serum indicators in PD. In addition, different modules related to fatty acid, lipid, pantothenate, and coenzyme A biosynthesis, and tyrosine and tryptophan metabolism were inferred from 16&#xa0;S rRNA data between PCI and PNCI. Both groups could be distinguished using models based on the abundance of Lactobacillaceae (Area under curve [AUC]&#x2009;=&#x2009;0.83), Actinomycetaceae (AUC&#x2009;=&#x2009;0.798), and Prevotellaceae (AUC&#x2009;=&#x2009;0.778) families and Lactobacillus (AUC&#x2009;=&#x2009;0.848) and Actinomyces (AUC&#x2009;=&#x2009;0.798) genera.<br><br>CONCLUSION: Gut microbiome evaluation could aid early cognitive impairment diagnosis in patients undergoing PD.}, }
@article {pmid38052752, year = {2023}, author = {Tom, A and Kumar, NP and Kumar, A and Saini, P}, title = {Interactions between Leishmania parasite and sandfly: a review.}, journal = {Parasitology research}, volume = {123}, number = {1}, pages = {6}, pmid = {38052752}, issn = {1432-1955}, support = {Fellowship/129/2022-ECD-II//Indian Council of Medical Research/ ; }, mesh = {Animals ; Humans ; *Leishmania ; *Psychodidae/parasitology ; *Parasites ; *Phlebotomus/parasitology ; *Leishmaniasis/parasitology ; Host-Parasite Interactions ; Mammals ; }, abstract = {Leishmaniasis transmission cycles are maintained and sustained in nature by the complex crosstalk of the Leishmania parasite, sandfly vector, and the mammalian hosts (human, as well as zoonotic reservoirs). Regardless of the vast research on human host-parasite interaction, there persists a substantial knowledge gap on the parasite's development and modulation in the vector component. This review focuses on some of the intriguing aspects of the Leishmania-sandfly interface, beginning with the uptake of the intracellular amastigotes from an infected host to the development of the parasite within the sandfly's alimentary canal, followed by the transmission of infective metacyclic stages to another potential host. Upon ingestion of the parasite, the sandfly hosts an intricate repertoire of immune barriers, either to evade the parasite or to ensure its homeostatic coexistence with the vector gut microbiome. Sandfly salivary polypeptides and Leishmania exosomes are co-egested with the parasite inoculum during the infected vector bite. This has been attributed to the modulation of the parasite infection and subsequent clinical manifestation in the host. While human host-based studies strive to develop effective therapeutics, a greater understanding of the vector-parasite-microbiome and human host interactions could help us to identify the targets and to develop strategies for effectively preventing the transmission of leishmaniasis.}, }
@article {pmid38052484, year = {2023}, author = {Singh, A and Schurman, SH and Bektas, A and Kaileh, M and Roy, R and Wilson, DM and Sen, R and Ferrucci, L}, title = {Aging and Inflammation.}, journal = {Cold Spring Harbor perspectives in medicine}, volume = {}, number = {}, pages = {}, doi = {10.1101/cshperspect.a041197}, pmid = {38052484}, issn = {2157-1422}, abstract = {Aging can be conceptualized as the progressive disequilibrium between stochastic damage accumulation and resilience mechanisms that continuously repair that damage, which eventually cause the development of chronic disease, frailty, and death. The immune system is at the forefront of these resilience mechanisms. Indeed, aging is associated with persistent activation of the immune system, witnessed by a high circulating level of inflammatory markers and activation of immune cells in the circulation and in tissue, a condition called "inflammaging." Like aging, inflammaging is associated with increased risk of many age-related pathologies and disabilities, as well as frailty and death. Herein we discuss recent advances in the understanding of the mechanisms leading to inflammaging and the intrinsic dysregulation of the immune function that occurs with aging. We focus on the underlying mechanisms of chronic inflammation, in particular the role of NF-κB and recent studies targeting proinflammatory mediators. We further explore the dysregulation of the immune response with age and immunosenescence as an important mechanistic immune response to acute stressors. We examine the role of the gastrointestinal microbiome, age-related dysbiosis, and the integrated stress response in modulating the inflammatory "response" to damage accumulation and stress. We conclude by focusing on the seminal question of whether reducing inflammation is useful and the results of related clinical trials. In summary, we propose that inflammation may be viewed both as a clinical biomarker of the failure of resilience mechanisms and as a causal factor in the rising burden of disease and disabilities with aging. The fact that inflammation can be reduced through nonpharmacological interventions such as diet and exercise suggests that a life course approach based on education may be a successful strategy to increase the health span with few adverse consequences.}, }
@article {pmid38052407, year = {2023}, author = {Nenu, I and Baldea, I and Coadă, CA and Craciun, RC and Moldovan, R and Tudor, D and Petrushev, B and Toma, VA and Stefanescu, H and Procopet, B and Sparchez, Z and Vodnar, D and Lenghel, M and Clichici, S and Filip, GA}, title = {Lactobacillus rhamnosus probiotic treatment modulates gut and liver inflammatory pathways in a hepatocellular carcinoma murine model. A preliminary study.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {}, number = {}, pages = {114314}, doi = {10.1016/j.fct.2023.114314}, pmid = {38052407}, issn = {1873-6351}, abstract = {BACKGROUND AND AIMS: Hepatocellular carcinoma (HCC) is a growing global concern with an increasing incidence rate. The intestinal microbiota has been identified as a potential culprit in modulating the effects of antitumoral drugs. We aimed to assess the impact of adding Lactobacillus rhamnosus probiotic to regorafenib in mice with HCC.<br><br>METHODS: Cirrhosis and HCCs were induced in 56 male Swiss mice via diethylnitrosamine injection and carbon tetrachloride administration. Mice were divided into four groups: treated with vehicle (VC), regorafenib (Rego), L. rhamnosus probiotic, and a combination of regorafenib and probiotic (Rego-Pro). After 3 weeks of treatment, liver and intestinal fragments were collected for analysis.<br><br>RESULTS: Regorafenib elevated gut permeability, an effect mitigated by probiotic intervention, which exhibited a notable correlation with reduced inflammation (p&#x202f;<&#x202f;0.01). iNOS levels were also reduced by adding the probiotic with respect to the mice treated with regorafenib only (p&#x202f;<&#x202f;0.001). Notably, regorafenib substantially increased IL-6, TNF-a and TLR4 in intestinal fragments (p&#x202f;<&#x202f;0.01). The administration of the probiotic effectively restored IL-6 to its initial levels (p&#x202f;<&#x202f;0.001).<br><br>CONCLUSION: Reducing systemic and intestinal inflammation by administering L. rhamnosus probiotic may alleviate tumoral resistance and systemic adverse effects.}, }
@article {pmid38052359, year = {2023}, author = {Dalton, KR and Lee, M and Wang, Z and Zhao, S and Parks, CG and Beane-Freeman, LE and Motsinger-Reif, AA and London, SJ}, title = {Occupational farm work activities influence workers' indoor home microbiome.}, journal = {Environmental research}, volume = {}, number = {}, pages = {117819}, doi = {10.1016/j.envres.2023.117819}, pmid = {38052359}, issn = {1096-0953}, abstract = {BACKGROUND: Farm work entails a heterogeneous mixture of exposures that vary considerably across farms and farmers. Farm work is associated with various health outcomes, both adverse and beneficial. One mechanism by which farming exposures can impact health is through the microbiome, including the indoor home environment microbiome. It is unknown how individual occupational exposures shape the microbial composition in workers' homes.<br><br>OBJECTIVES: We investigated associations between farm work activities, including specific tasks and pesticide use, and the indoor microbiome in the homes of 468 male farmers.<br><br>METHODS: Participants were licensed pesticide applicators, mostly farmers, enrolled in the Agricultural Lung Health Study from 2008 to 2011. Vacuumed dust from participants' bedrooms underwent whole-genome shotgun sequencing for indoor microbiome assessment. Using questionnaire data, we evaluated 6 farm work tasks (processing of either hay, silage, animal feed, fertilizer, or soy/grains, and cleaning grain bins) and 19 pesticide ingredients currently used in the past year, plus 7 banned persistent pesticide ingredients ever used.<br><br>RESULTS: All 6 work tasks were associated with increased microbial diversity levels, with a positive dose-response for the total number of tasks performed (P&#x202f;=&#x202f;0.001). All tasks were associated with altered microbial compositions (weighted UniFrac P&#x202f;=&#x202f;0.001) and with higher abundance of specific microbes, including soil-based commensal microbes such as Haloterrigena. Among the 19 pesticides, current use of glyphosate and past use of lindane were associated with increased microbial diversity (P&#x202f;=&#x202f;0.02-0.04). Ten currently used pesticides and all 7 banned pesticides were associated with altered microbial composition (P&#x202f;=&#x202f;0.001-0.04). Six pesticides were associated with differential abundance of certain microbes.<br><br>DISCUSSION: Different farm activities and exposures can uniquely impact the dust microbiome inside homes. Our work suggests that changes to the home microbiome could serve as one pathway for how occupational exposures impact the health of workers and their cohabitating family members, offering possible future intervention targets.}, }
@article {pmid38052127, year = {2023}, author = {Fernández Miyakawa, ME and Casanova, NA and Kogut, MH}, title = {How did antibiotic growth promoters increase growth and feed efficiency in poultry?.}, journal = {Poultry science}, volume = {103}, number = {2}, pages = {103278}, doi = {10.1016/j.psj.2023.103278}, pmid = {38052127}, issn = {1525-3171}, abstract = {It has been hypothesized that reducing the bioenergetic costs of gut inflammation as an explanation for the effect of antibiotic growth promoters (AGPs) on animal efficiency, framing some observations but not explaining the increase in growth rate or the prevention of infectious diseases. The host's ability to adapt to alterations in environmental conditions and to maintain health involves managing all physiological interactions that regulate homeostasis. Thus, metabolic pathways are vital in regulating physiological health as the energetic demands of the host guides most biological functions. Mitochondria are not only the metabolic heart of the cell because of their role in energy metabolism and oxidative phosphorylation, but also a central hub of signal transduction pathways that receive messages about the health and nutritional states of cells and tissues. In response, mitochondria direct cellular and tissue physiological alterations throughout the host. The endosymbiotic theory suggests that mitochondria evolved from prokaryotes, emphasizing the idea that these organelles can be affected by some antibiotics. Indeed, therapeutic levels of several antibiotics can be toxic to mitochondria, but subtherapeutic levels may improve mitochondrial function and defense mechanisms by inducing an adaptive response of the cell, resulting in mitokine production which coordinates an array of adaptive responses of the host to the stressor(s). This adaptive stress response is also observed in several bacteria species, suggesting that this protective mechanism has been preserved during evolution. Concordantly, gut microbiome modulation by subinhibitory concentration of AGPs could be the result of direct stimulation rather than inhibition of determined microbial species. In eukaryotes, these adaptive responses of the mitochondria to internal and external environmental conditions, can promote growth rate of the organism as an evolutionary strategy to overcome potential negative conditions. We hypothesize that direct and indirect subtherapeutic AGP regulation of mitochondria functional output can regulate homeostatic control mechanisms in a manner similar to those involved with disease tolerance.}, }
@article {pmid38051971, year = {2023}, author = {Haraoui, LP and Blaser, MJ}, title = {The Microbiome and Infectious Diseases.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {77}, number = {Supplement_6}, pages = {S441-S446}, doi = {10.1093/cid/ciad577}, pmid = {38051971}, issn = {1537-6591}, mesh = {Humans ; Animals ; *Microbiota ; Anti-Bacterial Agents/therapeutic use ; *Communicable Diseases/drug therapy ; *Hypersensitivity ; Obesity ; }, abstract = {Our perception of microbes has considerably changed since the recognition of their pathogenic potential in the 19th century. The discovery of antibiotics and their subsequent widespread adoption have substantially altered the landscape of medicine, providing us with treatment options for many infectious diseases and enabling the deployment of previously risky interventions (eg, surgical procedures and chemotherapy), while also leading to the rise of AMR. The latter is commonly viewed as the predominant downside of antibiotic use. However, with the increasing recognition that all metazoan organisms rely on a community of microbes (the microbiota) for normal development and for most physiologic processes, the negative impacts of antibiotic use now extend well beyond AMR. Using the iceberg as a metaphor, we argue that the effects of antibiotics on AMR represent the tip of the iceberg, with much greater repercussions stemming from their role in the rise of so-called noncommunicable diseases (including obesity, diabetes, allergic and autoimmune diseases, neurodevelopmental disorders, and certain cancers). We highlight some of the emerging science around the intersection of the microbiome, antibiotic use, and health (including biological costs and future therapeutic avenues), and we advocate a more nuanced approach in evaluating the impacts of proposed antibiotic use, especially in the setting of preexposure and postexposure prophylaxis.}, }
@article {pmid38051970, year = {2023}, author = {Gonzales-Luna, AJ and Carlson, TJ and Garey, KW}, title = {Review Article: Safety of Live Biotherapeutic Products Used for the Prevention of Clostridioides difficile Infection Recurrence.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {77}, number = {Supplement_6}, pages = {S487-S496}, doi = {10.1093/cid/ciad642}, pmid = {38051970}, issn = {1537-6591}, mesh = {Adult ; Humans ; *Clostridioides difficile ; Fecal Microbiota Transplantation/adverse effects ; *Clostridium Infections/microbiology ; Gastrointestinal Tract ; Feces/microbiology ; Recurrence ; }, abstract = {Live biotherapeutic products (LBPs) represent a new class of therapeutics indicated to prevent the recurrence of Clostridioides difficile infection (CDI) in adults. However, microbiota-based therapies have been used in CDI management before the Food and Drug Administration (FDA) designated this new drug class. The regulation of these microbiome-based therapies has varied, and several safety concerns have arisen over time. Requirements established by the FDA regarding the development of LBPs minimizes many of these prior concerns, and phase III trials have proven the safety and efficacy of 2 stool donor-derived LBPs: fecal microbiota, live-jslm (Rebyota™; formerly RBX2660) and fecal microbiota spores, live-brpk (Vowst™; formerly SER-109). Mild gastrointestinal side effects are common, but no severe drug-related adverse events have been reported with their use to date. A third LBP entering phase III clinical trials, VE303, follows a novel approach by sourcing bacterial strains from clonal cell banks and has demonstrated a similarly favorable safety profile.}, }
@article {pmid38051969, year = {2023}, author = {Anderson, SM and Sears, CL}, title = {The Role of the Gut Microbiome in Cancer: A Review, With Special Focus on Colorectal Neoplasia and Clostridioides difficile.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {77}, number = {Supplement_6}, pages = {S471-S478}, pmid = {38051969}, issn = {1537-6591}, support = {Y32-AI007291/NH/NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Clostridioides difficile ; Clostridioides ; *Colorectal Neoplasms ; *Microbiota ; Bacteria ; *Bacterial Toxins ; *Clostridium Infections/microbiology ; }, abstract = {The gut microbiome has coevolved with humans to aid in physiologic functions and prevent disease. An increasing prevalence of gut dysbiosis in modern society exists and has strong linkages to multiple disease processes common in the developed world. Mechanisms for microbiome-human interactions that impact host homeostasis include bacterial metabolite/toxin production, biofilm formation with mucous layer infiltration, and host immune system modulation. Most of this crosstalk occurs at the epithelial layer of the gut, and as such the role of these interactions in the induction of colorectal cancer-a highly prevalent disease globally and one undergoing significant epidemiologic shifts-is under increasing scrutiny. Although multiple individual gut bacteria have been hypothesized as possible driver organisms in the oncogenic process, no bacterium has been definitively identified as a causal agent of colorectal cancer, suggesting that host lifestyle factors, microbiome community interactions, and the mucosal and/or systemic immune response may play a critical role in the process. Recent evidence has emerged implicating the ubiquitous human pathogen Clostridioides difficile as a possible promoter of colorectal cancer through chronic toxin-mediated cellular changes. Although much remains to be defined regarding the natural history of infections caused by this pathogen and its potential for oncogenesis, it provides a strong model for the role of both individual bacteria and of the gut microbial community as a whole in the development of colorectal cancer.}, }
@article {pmid38051968, year = {2023}, author = {Reveles, KR and Strey, KA and Abdul-Mutakabbir, JC and Mendoza, VM and Carreno, JJ}, title = {Infectious Inequity: How the Gut Microbiome and Social Determinants of Health May Contribute to Clostridioides difficile Infection Among Racial and Ethnic Minorities.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {77}, number = {Supplement_6}, pages = {S455-S462}, pmid = {38051968}, issn = {1537-6591}, support = {//NIH)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Ethnic and Racial Minorities ; Social Determinants of Health ; *Communicable Diseases ; *Clostridium Infections/epidemiology ; }, abstract = {Infectious diseases are a leading contributor to death in the United States, and racial differences in clinical outcomes have been increasingly reported. Clostridioides difficile infection (CDI) is a growing public health concern, as it causes nearly half a million infections per year and considerable excess hospital costs. Concurrent with other infectious diseases, recent literature denotes racial disparities in CDI incidence rates, mortality, and associated morbidity. Of note, investigations into CDI and causative factors suggest that inequities in health-related social needs and other social determinants of health (SDoH) may cause disruption to the gut microbiome, thereby contributing to the observed deleterious outcomes in racially and ethnically minoritized individuals. Despite these discoveries, there is limited literature that provides context for the recognized racial disparities in CDI, particularly the influence of structural and systemic barriers. Here, we synthesize the available literature describing racial inequities in CDI outcomes and discuss the interrelationship of SDoH on microbiome dysregulation. Finally, we provide actionable considerations for infectious diseases professionals to aid in narrowing CDI equity gaps.}, }
@article {pmid38051967, year = {2023}, author = {Kelly, CR and Allegretti, JR}, title = {Review Article: Gastroenterology and Clostridium difficile Infection: Past, Present, and Future.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {77}, number = {Supplement_6}, pages = {S463-S470}, doi = {10.1093/cid/ciad644}, pmid = {38051967}, issn = {1537-6591}, mesh = {Humans ; Feces ; *Gastroenterology ; *Clostridioides difficile ; Gastrointestinal Tract ; *Clostridium Infections/therapy ; Fecal Microbiota Transplantation ; Recurrence ; Treatment Outcome ; }, abstract = {Research and innovation around Clostridium difficile infection (CDI) has been a multidisciplinary endeavor since discovery of the organism in 1978. The field of gastroenterology has contributed to our understanding of CDI as a disease caused by disruptions in the gut microbiome and led to advances in therapeutic manipulation of gut microbiota, including fecal microbiota transplantation. The high incidence of CDI in patients with inflammatory bowel disease and treatment of the infection in this population have been of particular interest to gastroenterologists. The emergence of standardized, approved live biotherapeutic products for treatment of recurrent CDI is an inflection point in our management of this difficult clinical problem, and real-world performance of these therapies will inform optimal treatment algorithms.}, }
@article {pmid38051966, year = {2023}, author = {}, title = {Video Introduction to "The Microbiome and Human Health Perspective".}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {77}, number = {Supplement_6}, pages = {e1}, doi = {10.1093/cid/ciad650}, pmid = {38051966}, issn = {1537-6591}, mesh = {Humans ; *Microbiota ; }, }
@article {pmid38051965, year = {2023}, author = {Nhu, NTQ and Young, VB}, title = {The Relationship Between the Microbiome and Antimicrobial Resistance.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {77}, number = {Supplement_6}, pages = {S479-S486}, doi = {10.1093/cid/ciad641}, pmid = {38051965}, issn = {1537-6591}, abstract = {Antibiotics have benefitted human health since their introduction nearly a century ago. However, the rise of antibiotic resistance may portend the dawn of the "post-antibiotic age." With the narrow pipeline for novel antimicrobials, we need new approaches to deal with the rise of multidrug resistant organisms. In the last 2 decades, the role of the intestinal microbiota in human health has been acknowledged and studied widely. Of the various activities carried out by the gut microbiota, colonization resistance is a key function that helps maintain homeostasis. Therefore, re-establishing a healthy microbiota is a novel strategy for treating drug resistance organisms. Preliminary studies suggest that this is a viable approach. However, the extent of their success still needs to be examined. Herein, we will review work in this area and suggest where future studies can further investigate this method for dealing with the threat of antibiotic resistance.}, }
@article {pmid38051964, year = {2023}, author = {Lavoie, T and Appaneal, HJ and LaPlante, KL}, title = {Advancements in Novel Live Biotherapeutic Products for Clostridioides difficile Infection Prevention.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {77}, number = {Supplement_6}, pages = {S447-S454}, doi = {10.1093/cid/ciad639}, pmid = {38051964}, issn = {1537-6591}, support = {//Seres and Ferring/ ; }, abstract = {The profound impact of the human microbiome on health and disease has captivated the interest of clinical and scientific communities. The human body hosts a vast array of microorganisms collectively forming the human microbiome, which significantly influences various physiological processes and profoundly shapes overall well-being. Notably, the gut stands out as an exceptional reservoir, harboring the most significant concentration of microorganisms, akin to an organ in itself. The gut microbiome's composition and function are influenced by genetics, environment, age, underlying conditions, and antibiotic usage, leading to dysbiosis and pathogenesis, such as Clostridioides difficile infection (CDI). Conventional CDI treatment, involving antibiotics like oral vancomycin and fidaxomicin, fails to address dysbiosis and may further disrupt gut microbial communities. Consequently, emerging therapeutic strategies are focused on targeting dysbiosis and restoring gut microbiota to advance CDI therapeutics. Fecal microbiota transplantation (FMT) has demonstrated remarkable efficacy in treating recurrent CDI by transferring processed stool from a healthy donor to a recipient, restoring gut dysbiosis and enhancing bacterial diversity. Moreover, 2 newer Food and Drug Administration (FDA)-approved live biotherapeutic products (LBP), namely, Fecal Microbiota Live-JSLM and Fecal Microbiota Spores Live-BRPK, have shown promise in preventing CDI recurrence. This review explores the role of the gut microbiota in preventing and treating CDI, with an emphasis on gut-based interventions like FMT and fecal microbiota-based products that hold potential for gut restoration and prevention of CDI recurrence. Understanding the microbiome's impact on CDI prevention and treatment offers valuable insights for advancing future CDI therapeutics.}, }
@article {pmid38051927, year = {2023}, author = {O'Dwyer, DN and Kim, JS and Ma, SF and Ranjan, P and Das, P and Lipinski, JH and Metcalf, JD and Falkowski, NR and Yow, E and Anstrom, K and Dickson, RP and Huang, Y and Gilbert, JA and Martinez, FJ and Noth, I}, title = {Commensal Oral Microbiota, Disease Severity and Mortality in Fibrotic Lung Disease.}, journal = {American journal of respiratory and critical care medicine}, volume = {}, number = {}, pages = {}, doi = {10.1164/rccm.202308-1357OC}, pmid = {38051927}, issn = {1535-4970}, abstract = {RATIONALE: Oral microbiota associate with diseases of the mouth and serve as a source of lung microbiota. However, the role of oral microbiota in lung disease is unknown.<br><br>OBJECTIVES: To determine associations between oral microbiota and disease severity and death in idiopathic pulmonary fibrosis.<br><br>METHODS: We analyzed 16S rRNA gene and shotgun metagenomic sequencing data of buccal swabs from 511 patients with idiopathic pulmonary fibrosis in the multicenter CleanUP-IPF trial. Buccal swabs were collected from usual care, and antimicrobial cohorts. Microbiome data was correlated with measures of disease severity using principal component analysis and linear regression models. Associations between the buccal microbiome and mortality were determined using Cox additive models, Kaplan Meier analysis and Cox proportional hazards models.<br><br>MEASUREMENTS AND MAIN RESULTS: Greater buccal microbial diversity associated with lower forced vital capacity (FVC) at baseline [mean diff -3.60: 95% CI -5.92 to -1.29 percent predicted FVC per 1 unit increment]. The buccal proportion of Streptococcus correlated positively with FVC [mean diff 0.80: 95% CI 0.16-1.43 percent predicted per 10% increase] (n=490). Greater microbial diversity was associated with an increased risk of death [HR 1.73: 95% CI 1.03-2.90] while a greater proportion of Streptococcus was associated with a reduced risk of death [HR 0.85: 95% CI 0.73 to 0.99]. The Streptococcus genus was mainly comprised of Streptococcus mitis species.<br><br>CONCLUSIONS: Increasing buccal microbial diversity predicts disease severity and death in IPF. The oral commensal Streptococcus mitis spp associates with preserved lung function and improved survival.}, }
@article {pmid38051704, year = {2023}, author = {Rubio-Garcia, A and Zomer, AL and Guo, R and Rossen, JWA and van Zeijl, JH and Wagenaar, JA and Luiken, REC}, title = {Characterising the gut microbiome of stranded harbour seals (Phoca vitulina) in rehabilitation.}, journal = {PloS one}, volume = {18}, number = {12}, pages = {e0295072}, doi = {10.1371/journal.pone.0295072}, pmid = {38051704}, issn = {1932-6203}, abstract = {Animal rehabilitation centres provide a unique opportunity to study the microbiome of wild animals because subjects will be handled for their treatment and can therefore be sampled longitudinally. However, rehabilitation may have unintended consequences on the animals' microbiome because of a less varied and suboptimal diet, possible medical treatment and exposure to a different environment and human handlers. Our study describes the gut microbiome of two large seal cohorts, 50 pups (0-30 days old at arrival) and 23 weaners (more than 60 days old at arrival) of stranded harbour seals admitted for rehabilitation at the Sealcentre Pieterburen in the Netherlands, and the effect of rehabilitation on it. Faecal samples were collected from all seals at arrival, two times during rehabilitation and before release. Only seals that did not receive antimicrobial treatment were included in the study. The average time in rehabilitation was 95 days for the pups and 63 days for the weaners. We observed that during rehabilitation, there was an increase in the relative abundance of some of the Campylobacterota spp and Actinobacteriota spp. The alpha diversity of the pups' microbiome increased significantly during their rehabilitation (p-value <0.05), while there were no significant changes in alpha diversity over time for weaners. We hypothesize that aging is the main reason for the observed changes in the pups' microbiome. At release, the sex of a seal pup was significantly associated with the microbiome's alpha (i.e., Shannon diversity was higher for male pups, p-value <0.001) and beta diversity (p-value 0.001). For weaners, variation in the microbiome composition (beta diversity) at release was partly explained by sex and age of the seal (p-values 0.002 and 0.003 respectively). We mainly observed variables known to change the gut microbiome composition (e.g., age and sex) and conclude that rehabilitation in itself had only minor effects on the gut microbiome of seal pups and seal weaners.}, }
@article {pmid38051644, year = {2023}, author = {Hou, T and Wang, Q and Dai, H and Hou, Y and Zheng, J and Wang, T and Lin, H and Wang, S and Li, M and Zhao, Z and Chen, Y and Xu, Y and Lu, J and Liu, R and Ning, G and Wang, W and Xu, M and Bi, Y}, title = {Interactive association between gut microbiota and thyroid cancer.}, journal = {Endocrinology}, volume = {}, number = {}, pages = {}, doi = {10.1210/endocr/bqad184}, pmid = {38051644}, issn = {1945-7170}, abstract = {CONTEXT: The association between the gut microbiota and thyroid cancer remains controversial.<br><br>OBJECTIVE: We aimed to systematically investigate the interactive causal relationships between the abundance and metabolism pathways of gut microbiota and thyroid cancer.<br><br>METHODS: We leveraged genome-wide association studies for the abundance of 211 microbiota taxa from the MiBioGen study (N&#x2009;=&#x2009;18,340), 205 microbiota metabolism pathways from the Dutch Microbiome Project (N&#x2009;=&#x2009;7738), and thyroid cancer from the Global Biobank Meta-analysis Initiative (N cases&#x2009;=&#x2009;6699 and N participants&#x2009;=&#x2009;1,620,354). We performed a bidirectional Mendelian randomization (MR) to investigate the causality from microbiota taxa and metabolism pathways to thyroid cancer, and vice versa. We performed a systematic review of previous observational studies and compared MR results with observational findings.<br><br>RESULTS: Eight taxa and twelve metabolism pathways had causal effects on thyroid cancer, where RuminococcaceaeUCG004 genus (P&#x2009;=&#x2009;0.001), Streptococcaceae family (P&#x2009;=&#x2009;0.016), Olsenella genus (P&#x2009;=&#x2009;0.029), ketogluconate metabolism pathway (P&#x2009;=&#x2009;0.003), pentose phosphate pathway (P&#x2009;=&#x2009;0.016), and L-arginine degradation II in AST pathway (P&#x2009;=&#x2009;0.0007) were supported by sensitivity analyses. Conversely, thyroid cancer had causal effects on three taxa and two metabolism pathways, where the Holdemanella genus (P&#x2009;=&#x2009;0.015) was supported by sensitivity analyses. The Proteobacteria phylum, Streptococcaceae family, Ruminococcus2 genus, and Holdemanella genus were significantly associated with thyroid cancer in both the systematic review and MR, while the other 121 significant taxa in observational results were not supported by MR.<br><br>DISCUSSIONS: These findings implicated the potential role of host-microbiota crosstalk in thyroid cancer, while the discrepancy among observational studies calls for further investigations.}, }
@article {pmid38051631, year = {2023}, author = {Jo, J and Hu, C and Begum, K and Wang, W and Le, TM and Agyapong, S and Hanson, BM and Ayele, H and Lancaster, C and Alam, MJ and Gonzales-Luna, AJ and Garey, KW}, title = {Fecal Pharmacokinetics and Gut Microbiome Effects of Oral Omadacycline versus Vancomycin in Healthy Volunteers.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiad537}, pmid = {38051631}, issn = {1537-6613}, abstract = {BACKGROUND: Clostridioides difficile infection is a common healthcare-associated infection with limited treatment options. Omadacycline, an aminomethylcycline tetracycline, has potent in vitro activity against C. difficile and a low propensity to cause Clostridioides difficile infection in clinical trials.<br><br>OBJECTIVES: To assess fecal pharmacokinetics and gut microbiome effects of oral omadacycline compared to oral vancomycin in healthy adults.<br><br>METHODS: This was a phase 1, non-blinded, randomized clinical trial conducted in healthy volunteers aged 18-40 years. Subjects received a 10-day course of omadacycline or vancomycin. Stool samples were collected at baseline, daily during therapy, and at follow up visits. Omadacycline and vancomycin stool concentrations were assessed, and microbiome changes were compared.<br><br>RESULTS: Sixteen healthy volunteers aged 26&#xb1;5 years (male: 63%; body mass index: 23.5&#xb1;4.0 kg/m2) were enrolled. Omadacycline was well tolerated with no safety signal differences between the two antibiotics. A rapid initial increase in fecal concentrations of omadacycline was observed compared to vancomycin, with maximum concentrations achieved within 48 hours. A significant difference in alpha diversity was observed following therapy in both omadacycline and vancomycin groups (p<0.05). Bacterial abundance and beta diversity analysis showed differing microbiome changes in subjects who received omadacycline versus vancomycin.<br><br>CONCLUSIONS: Subjects given omadacycline had high fecal concentrations with a distinct microbiome profile compared to vancomycin. These pharmacokinetic and microbiome properties may help explain its low risk to cause Clostridioides difficile infection and warrant further research into its development as an antibiotic for Clostridioides difficile treatment.}, }
@article {pmid38051352, year = {2023}, author = {Paintsil, EK and Masanta, WO and Dreyer, A and Ushanov, L and Smith, SI and Frickmann, H and Zautner, AE}, title = {Campylobacter in Africa - A specific viewpoint.}, journal = {European journal of microbiology &amp; immunology}, volume = {}, number = {}, pages = {}, doi = {10.1556/1886.2023.00043}, pmid = {38051352}, issn = {2062-509X}, abstract = {Campylobacter infections and campylobacteriosis-associated post-infectious sequelae are a significant global health burden that needs to be addressed from a specific African perspective. We conducted a comprehensive literature search on NCBI PubMed to compile a comprehensive narrative review article on Campylobacter infections in Africa, focusing on key aspects in human and veterinary medicine as well as food hygiene. We specifically focused on the epidemiology of enteropathogenic Campylobacter spp. in sub-Saharan and North Africa considering antimicrobial susceptibility. The most significant sequela resulting from molecular mimicry to Campylobacter surface structures is the Guillain-Barré syndrome, which was mainly examined in the context of limited studies conducted in African populations. A dedicated subsection is allocated to the limited research on the veterinary medically important species Campylobacter fetus. There are significant differences in the composition of the gut microbiome, especially in rural areas, which affect the colonization with Campylobacter spp. and the manifestation of campylobacteriosis. There may be a problem of overdiagnosis due to asymptomatic colonization, particularly in the detection of Campylobacter using molecular biological techniques. To reduce the colonization and infection rate of Campylobacter, we propose implementing several control measures and urge further research to improve the current understanding of the peculiarities of campylobacteriosis in Africa.}, }
@article {pmid38051055, year = {2023}, author = {Klementiev, AD and Garg, N and Whiteley, M}, title = {Identification of a glutathione transporter in A. actinomycetemcomitans.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0351123}, doi = {10.1128/spectrum.03511-23}, pmid = {38051055}, issn = {2165-0497}, abstract = {Microbes produce a large array of extracellular molecules, which serve as signals and cues to promote polymicrobial interactions and alter the function of microbial communities. This has been particularly well studied in the human oral microbiome, where key metabolites have been shown to impact both health and disease. Here, we used an untargeted mass spectrometry approach to comprehensively assess the extracellular metabolome of the pathogen Aggregatibacter actinomycetemcomitans and the commensal Streptococcus gordonii during mono- and co-culture. We generated and made publicly available a metabolomic data set that includes hundreds of potential metabolites and leveraged this data set to identify an operon important for glutathione secretion in A. actinomycetemcomitans.}, }
@article {pmid38051051, year = {2023}, author = {Custer, GF and Mealor, BA and Fowers, B and van Diepen, LTA}, title = {Failure to recover Pseudomonas fluorescens D7 supports claims of ineffectiveness as biocontrol agent of Bromus tectorum.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0177123}, doi = {10.1128/spectrum.01771-23}, pmid = {38051051}, issn = {2165-0497}, abstract = {Cheatgrass is one of North America's most problematic invasive species. Invasion by this annual grass alters ecosystem structure and function and has proven very challenging to remove with traditional approaches. Commercially available bioherbicides, like P. fluorescens D7, are applied with the goal of providing lasting control from a single application. However, experimental results suggest that this bioherbicide has limited efficacy under field conditions. Potential explanations for variable efficacy include a failure of this bioherbicide to establish in the soil microbiome. However, to our knowledge, no data exist to support or refute this hypothesis. Here, we use a deep-sequencing approach to better understand the effects of this bioherbicide on the soil microbiome and screen for P. fluorescens D7 at 18 months post-application.}, }
@article {pmid38050830, year = {2023}, author = {Yang, L and Liang, H and Wu, Q and Shen, P}, title = {Biochar alleviated the toxic effects of microplastics-contaminated geocarposphere soil on peanut (Arachis hypogaea L.) pod development: roles of pod nutrient metabolism and geocarposphere microbial modulation.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.13191}, pmid = {38050830}, issn = {1097-0010}, abstract = {BACKGROUND: The accumulation of microplastics in agricultural soil poses a threat to the sustainability of agriculture, impacting crop growth and soil health. Due to the geocarpy feature of peanut, geocarposphere soil environment is critical to pod development and its nutritional quality. While the effects of microplastics in the rhizosphere have been studied, their impact on peanut pod in the geocarposphere remains unknown. Biochar has emerged as a potential soil agents with the ability to remediate soil contamination. However, the mechanisms of biochar mitigated the toxic effects of microplastics-contaminated geocarposphere soil on peanut pod development remain largely unexplored.<br><br>RESULTS: We evaluated the peanut pod performance and microbiome when facing microplastics contamination and biochar amendment in geocarposphere soil. The results showed that microplastics present in geocarposphere soil could directly enter into the peanut pod, cause pod developmental disorder and exert adverse effects on nutritional quality. Aberrant expressions of key genes associated with amino acid metabolism, lipid synthesis, and auxin and ethylene signaling pathways were the underlying molecular mechanisms of microplastics-induced peanut pod developmental inhibition. However, these expression abnormalities could be reversed by biochar application. In addition, peanut geocarposphere microbiome results showed that biochar application could restore the diversity of microbial communities inhibited by microplastics contamination and promote the relative abundance of bacteria correlated with pathogen-resistance and nitrogen cycle of geocarposphere soil, further promoting peanut pod development.<br><br>CONCLUSION: This study demonstrated that biochar application is an effective strategy to mitigate the toxic effects of microplastics-contaminated geocarposphere soil on pod development and nutritional quality. This article is protected by copyright. All rights reserved.}, }
@article {pmid38050482, year = {2023}, author = {Byanova, KL and Abelman, R and North, CM and Christenson, SA and Huang, L}, title = {COPD in People with HIV: Epidemiology, Pathogenesis, Management, and Prevention Strategies.}, journal = {International journal of chronic obstructive pulmonary disease}, volume = {18}, number = {}, pages = {2795-2817}, pmid = {38050482}, issn = {1178-2005}, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/diagnosis/epidemiology/prevention &amp; control ; Risk Factors ; Lung ; Inflammation/complications ; *HIV Infections/diagnosis/drug therapy/epidemiology ; }, abstract = {Chronic obstructive pulmonary disease (COPD) is a progressive respiratory disorder characterized by airflow limitation and persistent respiratory symptoms. People with HIV (PWH) are particularly vulnerable to COPD development; PWH have demonstrated both higher rates of COPD and an earlier and more rapid decline in lung function than their seronegative counterparts, even after accounting for differences in cigarette smoking. Factors contributing to this HIV-associated difference include chronic immune activation and inflammation, accelerated aging, a predilection for pulmonary infections, alterations in the lung microbiome, and the interplay between HIV and inhalational toxins. In this review, we discuss what is known about the epidemiology and pathobiology of COPD among PWH and outline screening, diagnostic, prevention, and treatment strategies.}, }
@article {pmid38050344, year = {2023}, author = {Khor, AHP and Koguchi, T and Liu, H and Kakuta, M and Matsubara, D and Wen, R and Sagiya, Y and Imoto, S and Nakagawa, H and Matsuda, K and Tanikawa, C}, title = {Regulation of the innate immune response and gut microbiome by p53.}, journal = {Cancer science}, volume = {}, number = {}, pages = {}, doi = {10.1111/cas.15991}, pmid = {38050344}, issn = {1349-7006}, support = {JP23tm0624002//This research was supported by AMED under Grant Number/ ; JP233fa627011//This research was supported by AMED under Grant Number/ ; JP22zf0127009//This research was supported by AMED under Grant Number/ ; JP21ck0106693h0001//This research was supported by AMED under Grant Number/ ; JP21cm0106578//This research was supported by AMED under Grant Number/ ; JP23ck0106642//This research was supported by AMED under Grant Number/ ; JP19km0405215h0001//This research was supported by AMED under Grant Number/ ; JP16H02676//This work was supported by JSPS KAKENHI Grant Number/ ; JP19K22525//This work was supported by JSPS KAKENHI Grant Number/ ; //This study was supported by grants from the Takeda Science Foundation, the Hirose Foundation, and an academic scholarship from the Japan International Cooperation Agency./ ; }, abstract = {p53 is a key tumor suppressor mutated in half of human cancers. In recent years, p53 was shown to regulate a wide variety of functions. From the transcriptome analysis of 24 tissues of irradiated mice, we identified 553 genes markedly induced by p53. Gene Ontology (GO) enrichment analysis found that the most associated biological process was innate immunity. 16S rRNA-seq analysis revealed that Akkermansia, which has anti-inflammatory properties and is involved in the regulation of intestinal barrier integrity, was decreased in p53-knockout (p53[-/-]) mice after radiation. p53[-/-] mice were susceptible to radiation-induced GI toxicity and had a significantly shorter survival time than p53-wild-type (p53[+/+]) mice following radiation. However, administration of antibiotics resulted in a significant improvement in survival and protection against GI toxicity. Mbl2 and Lcn2, which have antimicrobial activity, were identified to be directly transactivated by p53 and secreted by liver into the circulatory system. We also found the expression of MBL2 and LCN2 was decreased in liver cancer tissues with p53 mutations compared with those without p53 mutations. These results indicate that p53 is involved in shaping the gut microbiome through its downstream targets related to the innate immune system, thus protecting the intestinal barrier.}, }
@article {pmid38050216, year = {2023}, author = {Zhu, Y and Ma, G and Ren, W and Hu, Z and Zhou, L and Zhang, X and Zhao, N and Zhang, M and Yan, L and Yu, Q and Liu, X and Chen, J}, title = {Effect of oral probiotics on clinical efficacy and intestinal flora in elderly severe pneumonia patients.}, journal = {Medicine}, volume = {102}, number = {48}, pages = {e36320}, pmid = {38050216}, issn = {1536-5964}, mesh = {Humans ; Aged ; *Gastrointestinal Microbiome ; Ecosystem ; Retrospective Studies ; *Probiotics/therapeutic use ; *Pneumonia/drug therapy ; Treatment Outcome ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {Complex microbial ecosystems in both gastrointestinal and respiratory systems have been found to have a significant impact on human health. Growing evidence has demonstrated that intestinal dysbiosis can increase vulnerability to pulmonary infections. However, changes in the composition and activity of the intestinal flora after probiotic supplementation may alter the disease state of the host. The effects of probiotics on the improvement of diseases, such as severe pneumonia (SP), in intensive care units (ICUs) remain controversial. We retrospectively included 88 patients diagnosed with severe pneumonia between April 2021 and June 2022. The patients were divided into 2 groups: a probiotic group (n = 40) and a control group (n = 48). In addition, changes in CRP, PCT, WBC, IL-6, Clostridium difficile toxin, and PSI pneumonia scores were assessed. Changes in the gut microbiome of the patients were assessed using amplicon sequencing. Compared to the control group, a significant reduction in the incidence of length of hospital stay was observed in the probiotic group, but there were no significant differences in the mortality rate, duration of fever, diarrhea, and constipation. After probiotic treatment, CRP, PCT, WBC, and PSI score were significantly lower than before, and better clinical efficacy was achieved in the probiotic group for the duration of antibiotic therapy. Gut microbiota analysis revealed that the abundance of opportunistic pathogens (e.g., Massilia) increased remarkably at the genus level in the control group, and a significant increase in Erysipelotrichaceae_ge was observed after probiotic intervention. The control group showed an increase in opportunistic pathogens (Citrobacter, Massilia) during the antibiotic treatment. Probiotics interventions inhibit the growth of opportunistic pathogens. In addition, we found that the population of butyrate-producing bacteria (e.g., Ruminococcaceae UCG-005) increased following probiotic treatment.}, }
@article {pmid38050061, year = {2023}, author = {Zhu, J and Sun, C and Li, M and Hu, G and Zhao, XM and Chen, WH}, title = {Compared to histamine-2 receptor antagonist, proton pump inhibitor induces stronger oral-to-gut microbial transmission and gut microbiome alterations: a randomised controlled trial.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2023-330168}, pmid = {38050061}, issn = {1468-3288}, abstract = {OBJECTIVE: We aim to compare the effects of proton pump inhibitors (PPIs) and histamine-2 receptor antagonists (H2RAs) on the gut microbiota through longitudinal analysis.<br><br>DESIGN: Healthy volunteers were randomly assigned to receive either PPI (n=23) or H2RA (n=26) daily for seven consecutive days. We collected oral (saliva) and faecal samples before and after the intervention for metagenomic next-generation sequencing. We analysed intervention-induced alterations in the oral and gut microbiome including microbial abundance and growth rates, oral-to-gut transmissions, and compared differences between the PPI and H2RA groups.<br><br>RESULTS: Both interventions disrupted the gut microbiota, with PPIs demonstrating more pronounced effects. PPI usage led to a significantly higher extent of oral-to-gut transmission and promoted the growth of specific oral microbes in the gut. This led to a significant increase in both the number and total abundance of oral species present in the gut, including the identification of known disease-associated species like Fusobacterium nucleatum and Streptococcus anginosus. Overall, gut microbiome-based machine learning classifiers could accurately distinguish PPI from non-PPI users, achieving an area under the receiver operating characteristic curve (AUROC) of 0.924, in contrast to an AUROC of 0.509 for H2RA versus non-H2RA users.<br><br>CONCLUSION: Our study provides evidence that PPIs have a greater impact on the gut microbiome and oral-to-gut transmission than H2RAs, shedding light on the mechanism underlying the higher risk of certain diseases associated with prolonged PPI use.<br><br>TRIAL REGISTRATION NUMBER: ChiCTR2300072310.}, }
@article {pmid38049632, year = {2023}, author = {Schäffer, DE and Li, W and Elbasir, A and Altieri, DC and Long, Q and Auslander, N}, title = {Microbial gene expression analysis of healthy and cancerous esophagus uncovers bacterial biomarkers of clinical outcomes.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {128}, pmid = {38049632}, issn = {2730-6151}, support = {R00CA252025//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; RF1-AG063481//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; }, abstract = {Local microbiome shifts are implicated in the development and progression of gastrointestinal cancers, and in particular, esophageal carcinoma (ESCA), which is among the most aggressive malignancies. Short-read RNA sequencing (RNAseq) is currently the leading technology to study gene expression changes in cancer. However, using RNAseq to study microbial gene expression is challenging. Here, we establish a new tool to efficiently detect viral and bacterial expression in human tissues through RNAseq. This approach employs a neural network to predict reads of likely microbial origin, which are targeted for assembly into longer contigs, improving identification of microbial species and genes. This approach is applied to perform a systematic comparison of bacterial expression in ESCA and healthy esophagi. We uncover bacterial genera that are over or underabundant in ESCA vs healthy esophagi both before and after correction for possible covariates, including patient metadata. However, we find that bacterial taxonomies are not significantly associated with clinical outcomes. Strikingly, in contrast, dozens of microbial proteins were significantly associated with poor patient outcomes and in particular, proteins that perform mitochondrial functions and iron-sulfur coordination. We further demonstrate associations between these microbial proteins and dysregulated host pathways in ESCA patients. Overall, these results suggest possible influences of bacteria on the development of ESCA and uncover new prognostic biomarkers based on microbial genes. In addition, this study provides a framework for the analysis of other human malignancies whose development may be driven by pathogens.}, }
@article {pmid38049401, year = {2023}, author = {Baig, Y and Ma, HR and Xu, H and You, L}, title = {Autoencoder neural networks enable low dimensional structure analyses of microbial growth dynamics.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7937}, pmid = {38049401}, issn = {2041-1723}, support = {R01AI125604//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01GM098642//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01EB031869//U.S. Department of Health &amp; Human Services | NIH | National Institute of Biomedical Imaging and Bioengineering (NIBIB)/ ; HR0011-23-2-0008//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; }, mesh = {*Neural Networks, Computer ; Machine Learning ; Bacteria/genetics ; *Microbiota ; }, abstract = {The ability to effectively represent microbiome dynamics is a crucial challenge in their quantitative analysis and engineering. By using autoencoder neural networks, we show that microbial growth dynamics can be compressed into low-dimensional representations and reconstructed with high fidelity. These low-dimensional embeddings are just as effective, if not better, than raw data for tasks such as identifying bacterial strains, predicting traits like antibiotic resistance, and predicting community dynamics. Additionally, we demonstrate that essential dynamical information of these systems can be captured using far fewer variables than traditional mechanistic models. Our work suggests that machine learning can enable the creation of concise representations of high-dimensional microbiome dynamics to facilitate data analysis and gain new biological insights.}, }
@article {pmid38049273, year = {2024}, author = {Mantegazza, G and Duncan, R and Telesca, N and Gargari, G and Perotti, S and Riso, P and Guglielmetti, S}, title = {Lactic acid bacteria naturally associated with ready-to-eat rocket salad can survive the human gastrointestinal transit.}, journal = {Food microbiology}, volume = {118}, number = {}, pages = {104418}, doi = {10.1016/j.fm.2023.104418}, pmid = {38049273}, issn = {1095-9998}, mesh = {Humans ; *Lactobacillales ; *Salads ; Food Microbiology ; Gastrointestinal Transit ; Vegetables/microbiology ; Bacteria ; Leuconostoc ; }, abstract = {It was theorized that modernization and the decline in harmless microbial populations associated with food have altered the gut microbiota, impacting host metabolism and immunity. Western dietary patterns, characterized by processed foods and preservation methods, may significantly reduce the microbial population associated with food. To mitigate the consequences of bacterial deprivation, the integration of these diets with fermented foods is commonly proposed. Nonetheless, non-fermented food consumed raw may also be an important source of viable microbial cells for the human microbiome. This study investigates whether salad-associated LAB can survive the gastrointestinal transit (GIT) and contribute to the gut microbiota. LAB strains were quantified and isolated from rocket salad (Eruca vesicaria subsp. sativa), and their survival through GIT was assessed via intervention trials in healthy adults and in vitro. Moreover, bacterial communities in fecal samples were analyzed after three days of rocket salad consumption. Washing with a sodium hypochlorite solution drastically reduced total bacterial load and eliminated viable LAB. The quantity of LAB introduced through salads did not significantly alter the gut microbiota composition. Rocket salads harbored Weissella and Leuconostoc species. A significant increase in Weissella spp. but not in Leuconostoc spp. was observed after the consumption of rocket salad. Simulated GIT experiments suggested that the food matrix and the initial number of ingested viable bacteria may have been important in determining survival. These findings propose that plant products could serve as sources of live LAB for the human gut. Further research with diverse vegetables and longer interventions is needed, encouraging studies on raw, non-fermented foods and their impact on the human intestinal microbiome.}, }
@article {pmid38048996, year = {2023}, author = {Jia, Q and Wang, H and Wang, Y and Xue, W and Jiang, Q and Wang, J and Ning, F and Zhu, Z and Tian, L}, title = {Investigation of the mechanism of silica-induced pulmonary fibrosis: The role of lung microbiota dysbiosis and the LPS/TLR4 signaling pathway.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {168948}, doi = {10.1016/j.scitotenv.2023.168948}, pmid = {38048996}, issn = {1879-1026}, abstract = {The widespread manufacture of silica and its extensive use, and potential release of silica into the environment pose a serious human health hazard. Silicosis, a severe global public health issue, is caused by exposure to silica, leading to persistent inflammation and fibrosis of the lungs. The underlying pathogenic mechanisms of silicosis remain elusive. Lung microbiota dysbiosis is associated with the development of inflammation and fibrosis. However, limited information is currently available regarding the role of lung microbiota in silicosis. The study therefore is designed to conduct a comprehensive analysis of the role of lung microbiota dysbiosis and establish a basis for future investigations into the potential mechanisms underlying silicosis. Here, the pathological and biochemical parameters were used to systematically assessed the degree of inflammation and fibrosis following silica exposure and treatment with combined antibiotics. The underlying mechanisms were studied via integrative multi-omics analyses of the transcriptome and microbiome. Analysis of 16S ribosomal DNA revealed dysbiosis of the microbial community in silicosis, characterized by a predominance of gram-negative bacteria. Exposure to silica has been shown to trigger lung inflammation and fibrosis, leading to an increased concentration of lipopolysaccharides in the bronchoalveolar lavage fluid. Furthermore, Toll-like receptor 4 was identified as a key molecule in the lung microbiota dysbiosis associated with silica-induced lung fibrosis. All of these outcomes can be partially controlled through combined antibiotic administration. The study findings demonstrate that the dysbiosis of lung microbiota enhances silica-induced fibrosis associated with the lipopolysaccharides/Toll-like receptor 4 pathway and provided a promising target for therapeutic intervention of silicosis.}, }
@article {pmid38048923, year = {2023}, author = {Che, H and Wang, X and He, S and Dong, X and Lv, L and Xie, W and Li, H}, title = {Orally administered selenium-containing α-D-1,6-glucan and α-D-1,6-glucan relief early cognitive deficit in APP/PS1 mice.}, journal = {International journal of biological macromolecules}, volume = {257}, number = {Pt 1}, pages = {128539}, doi = {10.1016/j.ijbiomac.2023.128539}, pmid = {38048923}, issn = {1879-0003}, abstract = {Alzheimer's disease (AD) is a complex, progressive and deadly disorder that exhibits various typical pathological characteristics. Till now no effective treatment has been found that can prevent or reverse AD. Here, the effects of 2 months of treatment with α-D-1,6-glucan (CPA) and selenium-containing α-D-1,6-glucan (Se-CPA) on early cognitive dysfunction and neuropathology were explored in the 3-month-old APP/PS1 transgenic mouse. The results of the Morris water maze and open-field test revealed that Se-CPA exerted more significant effects than CPA in improving cognitive function and depressive-like behavior by attenuating the oxidative stress, decreasing serum LPS level, downregulating the inflammation of astrocytes and microglia through inhibiting the activation of NLRP3 inflammasome, mitigating neuronal cells loss and improving synaptic plasticity. Moreover, Se-CPA exerted beneficial effects on reshaping gut microbiome by increasing the microbial α-diversity, enhancing the proportion of beneficial bacteria such as Akkermansia muciniphila and promoting the SCFAs concentration. These findings provide evidence that Se-CPA might be a potentially viable compound for AD prevention.}, }
@article {pmid38048922, year = {2023}, author = {Zhao, K and Wu, X and Han, G and Sun, L and Zheng, C and Hou, H and Xu, BB and El-Bahy, ZM and Qian, C and Kallel, M and Algadi, H and Guo, Z and Shi, Z}, title = {Phyllostachys nigra (Lodd. ex Lindl.) derived polysaccharide with enhanced glycolipid metabolism regulation and mice gut microbiome.}, journal = {International journal of biological macromolecules}, volume = {257}, number = {Pt 1}, pages = {128588}, doi = {10.1016/j.ijbiomac.2023.128588}, pmid = {38048922}, issn = {1879-0003}, abstract = {This study focuses on the characterization and regulation of glycolipid metabolism of polysaccharides derived from biomass of Phyllostachys nigra (Lodd. ex Lindl.) root (PNr). The extracts from dilute hydrochloric acid, hot water, and 2 % sodium hydroxide solution were characterized through molecular weight, gel permeation chromatography, monosaccharides, Fourier transform infrared, and nuclear magnetic resonance spectroscopy analyses. Polysaccharide from alkali extraction and molecular sieve purification (named as: PNS2A) exhibited optimal inhibitory of 3T3-L1 cellular differentiation and lowered insulin resistance. The PNS2A is made of a hemicellulose-like main chain of →4)-β-D-Xylp-(1→ that was connected by branches of 4-O-Me-α-GlcAp-(1→, T-α-D-Galp-(1→, T-α-L-Araf-(1→, →2)-α-L-Araf-(1→, as well as β-D-Glcp-(1→4-β-D-Glcp-(1→ fragments. Oral delivery of PNS2A in diabetes mice brought down blood glucose and cholesterol levels and regulated glucose and lipid metabolism. PNS2A alleviated diabetes symptoms and body weight and protected liver and kidney function in model animals by altering the gut microbiome. Polysaccharides can be a new approach to develop bamboo resources.}, }
@article {pmid38048888, year = {2023}, author = {Hocquigny, A and Hugerot, H and Ghanem, R and Haute, T and Laurent, V and Cogulet, V and Montier, T}, title = {Mucoactive drugs and multiple applications in pulmonary disease therapy.}, journal = {European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ejpb.2023.12.001}, pmid = {38048888}, issn = {1873-3441}, abstract = {Mucus is a complex polymeric hydrogel that serves as a critical defense in several organs. In the lungs, it provides a formidable barrier against inhaled particles such as microorganisms. In addition, mucus is essential for normal lung physiology, as it promotes immune tolerance and facilitates a normal commensal pulmonary microbiome. Hypersecretion of airway mucus is a characteristic of numerous respiratory diseases, such as Chronic Obstructive Pulmonary Disease (COPD) and Cystic Fibrosis (CF), and creates pulmonary obstruction, limiting the effectiveness of inhaled therapies. Due to those alterations, therapeutic strategies must be optimal to limit airway obstruction and restore pulmonary function. Mucoactive drugs are common therapeutic options and are classified into different groups depending on their modes of action, i.e., expectorants, mucokinetics, mucoregulators and mucolytics. This review focuses on mucoactive drugs and their modes of action. A special focus will be made on two challenging pulmonary pathologies: COPD and CF, and on their clinical studies conducted with mucoactive drugs.}, }
@article {pmid38048871, year = {2023}, author = {Lan, W and Liu, H and Weng, R and Zeng, Y and Lou, J and Xu, H and Yu, Y and Jiang, Y}, title = {Microbial community of municipal drinking water in Hangzhou using metagenomic sequencing.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {123066}, doi = {10.1016/j.envpol.2023.123066}, pmid = {38048871}, issn = {1873-6424}, abstract = {While traditional culture-dependent methods can effectively detect certain microorganisms, the comprehensive composition of the municipal drinking water (DW) microbiome, including bacteria, archaea, and viruses, remains unknown. Metagenomic sequencing has opened the door to accurately determine and analyze the entire microbial community of DW, providing a comprehensive understanding of DW species diversity, especially in the context of public health concerns during the COVID-19 era. In this study, we found that most of the culturable bacteria and some fecal indicator bacteria, such as Escherichia coli and Pseudomonas aeruginosa, were non-culturable using culture-dependent methods in all samples. However, metagenomic analysis showed that the predominant bacterial species in the DW samples belonged to the phyla Proteobacteria and Planctomycetes. Notably, the genus Methylobacterium was the most abundant in all water samples, followed by Sphingomonas, Gemmata, and Azospirilum. While low levels of virulence-associated factors, such as the Esx-5 type VII secretion system (T7SS) and DevR/S, were detected, only the erythromycin resistance gene erm(X), an rRNA methyltransferase, was identified at low abundance in one sample. Hosts corresponding to virulence and resistance genes were identified in some samples, including Mycobacterium spp. Archaeal DNA (Euryarchaeota, Crenarchaeota) was found in trace amounts in some DW samples. Viruses such as rotavirus, coxsackievirus, human enterovirus, and SARS-CoV-2 were negative in all DW samples using colloidal gold and real-time reverse transcription polymerase chain reaction (RT‒PCR) methods. However, DNA encoding a new order of reverse-transcribing viruses (Ortervirales) and Herpesvirales was found in some DW samples. The metabolic pathways of the entire microbial community involve cell‒cell communication and signal secretion, contributing to cooperation between different microbial populations in the water. This study provides insight into the microbial community and metabolic process of DW in Hangzhou, China, utilizing both culture-dependent methods and metagenomic sequencing combined with bioinformatics tools during the COVID-19 pandemic era.}, }
@article {pmid38048833, year = {2023}, author = {Pamanji, R and Kumareshan, TN and Priya S, L and Sivan, G and Selvin, J}, title = {Exploring the impact of antibiotics, microplastics, nanoparticles, and pesticides on zebrafish gut microbiomes: Insights into composition, interactions, and health implications.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {140867}, doi = {10.1016/j.chemosphere.2023.140867}, pmid = {38048833}, issn = {1879-1298}, abstract = {This reviewdu addresses the impact of various chemical entities like pesticides, antibiotics, nanoparticles and microplastic on gut microbiota of zebrafish. Gut microbiota plays a vital role in metabolic regulation in every organism. As majority of metabolic pathways coordinated by microbiota, small alterations associated with mild to serious outcomes. Because of their unstoppable usage in day-to-day life, the present-day research on gut microbiota is mostly comprising aforementioned chemicals. It is better to understand how gut microbiome is dysbiosed by various environmental factors, to keep our microbiota safe. We tried to delineate the natural flora of zebrafish gut microbiome and the metabolic and other pathways associated and what are the common flora that was dysbiosed during the treatment. Based on the existing literature, we reviewed pesticides like Imazalil, Difenoconazole, Chlorpyrifos, Metamifop, Carbendazim, Imidacloprid, Phoxim, Niclosamide, Dieldrin, and antibiotics like Oxytetracycline, Enrofloxacin, Florfenicol, Sulfamethoxazole, Tetracycline, Streptomycin, Doxycycline, and in the category of nanoparticles, Titanium dioxide nanoparticles (nTiO2), Abalone viscera hydrolysates decorated silver nanoparticles (AVH-AgNPs), Lead-halide perovskite nanoparticles (LHP NPs), Copper nanoparticles (Cu-NPs), silver nanoparticles (Ag-NPs) and microplastic types like polyethylene and polystyrene microplastic. Other studies with miscellaneous chemical entities on zebrafish gut microbiome include Ferulic acid, Polychlorinated biphenyls, Cadmium, Disinfection by-products, Triclosan, microcystin-LR, Fluoride, and Amitriptyline.}, }
@article {pmid38048456, year = {2023}, author = {Winter, SE and Bäumler, AJ}, title = {Gut dysbiosis: Ecological causes and causative effects on human disease.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {50}, pages = {e2316579120}, doi = {10.1073/pnas.2316579120}, pmid = {38048456}, issn = {1091-6490}, support = {AI118807//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI166263//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI171537//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI044170//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI096528//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI112445//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI112949//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI146432//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI153069//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1017880//Burroughs Wellcome Fund (BWF)/ ; 2021025//United States - Israel Binational Science Foundation (BSF)/ ; 20230029//Kenneth Rainin Foundation (KRF)/ ; }, mesh = {Humans ; Dysbiosis ; *Microbiota ; *Gastrointestinal Microbiome ; }, abstract = {The gut microbiota plays a role in many human diseases, but high-throughput sequence analysis does not provide a straightforward path for defining healthy microbial communities. Therefore, understanding mechanisms that drive compositional changes during disease (gut dysbiosis) continues to be a central goal in microbiome research. Insights from the microbial pathogenesis field show that an ecological cause for gut dysbiosis is an increased availability of host-derived respiratory electron acceptors, which are dominant drivers of microbial community composition. Similar changes in the host environment also drive gut dysbiosis in several chronic human illnesses, and a better understanding of the underlying mechanisms informs approaches to causatively link compositional changes in the gut microbiota to an exacerbation of symptoms. The emerging picture suggests that homeostasis is maintained by host functions that control the availability of resources governing microbial growth. Defining dysbiosis as a weakening of these host functions directs attention to the underlying cause and identifies potential targets for therapeutic intervention.}, }
@article {pmid38048079, year = {2023}, author = {Fu, P and Wu, Y and Zhang, Z and Qiu, Y and Wang, Y and Peng, Y}, title = {VIGA: a one-stop tool for eukaryotic virus identification and genome assembly from next-generation-sequencing data.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {1}, pages = {}, doi = {10.1093/bib/bbad444}, pmid = {38048079}, issn = {1477-4054}, support = {32370700//National Natural Science Foundation of China/ ; 2022YFC2303802//National Key Plan for Scientific Research and Development of China/ ; }, mesh = {Humans ; High-Throughput Nucleotide Sequencing ; *Colitis, Ulcerative ; *Crohn Disease ; Genome, Viral ; Metagenome ; }, abstract = {Identification of viruses and further assembly of viral genomes from the next-generation-sequencing data are essential steps in virome studies. This study presented a one-stop tool named VIGA (available at https://github.com/viralInformatics/VIGA) for eukaryotic virus identification and genome assembly from NGS data. It was composed of four modules, namely, identification, taxonomic annotation, assembly and novel virus discovery, which integrated several third-party tools such as BLAST, Trinity, MetaCompass and RagTag. Evaluation on multiple simulated and real virome datasets showed that VIGA assembled more complete virus genomes than its competitors on both the metatranscriptomic and metagenomic data and performed well in assembling virus genomes at the strain level. Finally, VIGA was used to investigate the virome in metatranscriptomic data from the Human Microbiome Project and revealed different composition and positive rate of viromes in diseases of prediabetes, Crohn's disease and ulcerative colitis. Overall, VIGA would help much in identification and characterization of viromes, especially the known viruses, in future studies.}, }
@article {pmid38047905, year = {2023}, author = {Chen, S and He, F and Cheng, X}, title = {Analysis of subgingival bacterial and fungal diversity in patients with peri-implantitis based on 16sRNA and internal transcribed spacer sequencing.}, journal = {Future microbiology}, volume = {}, number = {}, pages = {}, doi = {10.2217/fmb-2023-0228}, pmid = {38047905}, issn = {1746-0921}, abstract = {Aim: To analyze subgingival fungal diversity in peri-implant inflammation patients and their relationship with bacteria. Methods: We collected saliva samples from four groups. 16sRNA and internal transcribed spacer sequencing was performed preceded by quantitative PCR and enzyme-linked immunosorbent assay tests. Analyses were done using R and Cytoscape software. Results: Significant differences were observed in the Abundance-based Coverage Estimator (ACE) index between control and peri-implantitis samples. Basidiomycota was the dominant fungal species, while Firmicutes dominated the bacteria. The most abundant fungal and bacterial species were 's_unclassified g Apiotrichum' and 's_unclassified g Streptococcus', respectively. Dothiorella was strongly associated with immunoglobulin G levels, with positive correlations between specific microorganisms and peri-implantitis in Q-PCR. Conclusion: Our findings have significant clinical implications, suggesting specific fungal and bacterial taxa roles in peri-implant inflammation.}, }
@article {pmid38047486, year = {2023}, author = {Shankar, A and Deal, CK and McCahon, S and Callegari, K and Seitz, T and Yan, L and Drown, DM and Williams, CT}, title = {SAD rats: Effects of short photoperiod and carbohydrate consumption on sleep, liver steatosis, and the gut microbiome in diurnal grass rats.}, journal = {Chronobiology international}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/07420528.2023.2288223}, pmid = {38047486}, issn = {1525-6073}, abstract = {Seasonal affective disorder (SAD) is a recurrent depression triggered by exposure to short photoperiods, with a subset of patients reporting hypersomnia, increased appetite, and carbohydrate craving. Dysfunction of the microbiota - gut - brain axis is frequently associated with depressive disorders, but its role in SAD is unknown. Nile grass rats (Arvicanthis niloticus) are potentially useful for exploring the pathophysiology of SAD, as they are diurnal and have been found to exhibit anhedonia and affective-like behavior in response to short photoperiods. Further, given grass rats have been found to spontaneously develop metabolic syndrome, they may be particularly susceptible to environmental triggers of metabolic dysbiosis. We conducted a 2 × 2 factorial design experiment to test the effects of short photoperiod (4 h:20 h Light:Dark (LD) vs. neutral 12:12 LD), access to a high concentration (8%) sucrose solution, and the interaction between the two, on activity, sleep, liver steatosis, and the gut microbiome of grass rats. We found that animals on short photoperiods maintained robust diel rhythms and similar subjective day lengths as controls in neutral photoperiods but showed disrupted activity and sleep patterns (i.e. a return to sleep after an initial bout of activity that occurs ~ 13 h before lights off). We found no evidence that photoperiod influenced sucrose consumption. By the end of the experiment, some grass rats were overweight and exhibited signs of non-alcoholic fatty liver disease (NAFLD) with micro- and macro-steatosis. However, neither photoperiod nor access to sucrose solution significantly affected the degree of liver steatosis. The gut microbiome of grass rats varied substantially among individuals, but most variation was attributable to parental effects and the microbiome was unaffected by photoperiod or access to sucrose. Our study indicates short photoperiod leads to disrupted activity and sleep in grass rats but does not impact sucrose consumption or exacerbate metabolic dysbiosis and NAFLD.}, }
@article {pmid38047281, year = {2023}, author = {Archer, D and Perez-Muñoz, ME and Tollenaar, S and Veniamin, S and Cheng, CC and Richard, C and Barreda, DR and Field, CJ and Walter, J}, title = {The importance of the timing of microbial signals for perinatal immune system development.}, journal = {Microbiome research reports}, volume = {2}, number = {2}, pages = {11}, pmid = {38047281}, issn = {2771-5965}, abstract = {Background: Development and maturation of the immune system begin in utero and continue throughout the neonatal period. Both the maternal and neonatal gut microbiome influence immune development, but the relative importance of the prenatal and postnatal periods is unclear. Methods: In the present study, we characterized immune cell populations in mice in which the timing of microbiome colonization was strictly controlled using gnotobiotic methodology. Results: Compared to conventional (CONV) mice, germ-free (GF) mice conventionalized at birth (EC mice) showed few differences in immune cell populations in adulthood, explaining only 2.36% of the variation in immune phenotypes. In contrast, delaying conventionalization to the fourth week of life (DC mice) affected seven splenic immune cell populations in adulthood, including dendritic cells and regulatory T cells (Tregs), explaining 29.01% of the variation in immune phenotypes. Early life treatment of DC mice with Limosilactobacillus reuteri restored splenic dendritic cells and Tregs to levels observed in EC mice, and there were strain-specific effects on splenic CD4+ T cells, CD8+ T cells, and CD11c+ F4/80+ mononuclear phagocytes. Conclusion: This work demonstrates that the early postnatal period, compared to the prenatal period, is relatively more important for microbial signals to influence immune development in mice. Our findings further show that targeted microbial treatments in early life can redress adverse effects on immune development caused by the delayed acquisition of the neonatal gut microbiome.}, }
@article {pmid38047280, year = {2023}, author = {Ladeira, R and Tap, J and Derrien, M}, title = {Exploring Bifidobacterium species community and functional variations with human gut microbiome structure and health beyond infancy.}, journal = {Microbiome research reports}, volume = {2}, number = {2}, pages = {9}, pmid = {38047280}, issn = {2771-5965}, abstract = {Aim: The human gut Bifidobacterium community has been studied in detail in infants and following dietary interventions in adults. However, the variability of the distribution of Bifidobacterium species and intra-species functions have been little studied, particularly beyond infancy. Here, we explore the ecology of Bifidobacterium communities in a large public dataset of human gut metagenomes, mostly corresponding to adults. Methods: We selected 9.515 unique gut metagenomes from curatedMetagenomicData. Samples were partitioned by applying Dirichlet's multinomial mixture to Bifidobacterium species. A functional analysis was performed on > 2.000 human-associated Bifidobacterium metagenome-assembled genomes (MAGs) paired with participant gut microbiome and health features. Results: We identified several Bifidobacterium-based partitions in the human gut microbiome differing in terms of the presence and abundance of Bifidobacterium species. The partitions enriched in both B. longum and B. adolescentis were associated with gut microbiome diversity and a higher abundance of butyrate producers and were more prevalent in healthy individuals. B. bifidum MAGs harboring a set of genes potentially related to phages were more prevalent in partitions associated with a lower gut microbiome diversity and were genetically more closely related. Conclusion: This study expands our knowledge of the ecology and variability of the Bifidobacterium community, particularly in adults, and its specific association with the gut microbiota and health. Its findings may guide the rational selection of Bifidobacterium strains for gut microbiome complementation according to the individual's endogenous Bifidobacterium community. Our results also suggest that gut microbiome stratification for particular genera may be relevant for studies of variations of species and associations with the gut microbiome and health.}, }
@article {pmid38047279, year = {2023}, author = {Candeliere, F and Musmeci, E and Amaretti, A and Sola, L and Raimondi, S and Rossi, M}, title = {Profiling of the intestinal community of Clostridia: taxonomy and evolutionary analysis.}, journal = {Microbiome research reports}, volume = {2}, number = {2}, pages = {13}, pmid = {38047279}, issn = {2771-5965}, abstract = {Aim: Clostridia are relevant commensals of the human gut due to their major presence and correlations to the host. In this study, we investigated intestinal Clostridia of 51 healthy subjects and reconstructed their taxonomy and phylogeny. The relatively small number of intestinal Clostridia allowed a systematic whole genome approach based on average amino acid identity (AAI) and core genome with the aim of revising the current classification into genera and determining evolutionary relationships. Methods: 51 healthy subjects' metagenomes were retrieved from public databases. After the dataset's validation through comparison with Human Microbiome Project (HMP) samples, the metagenomes were profiled using MetaPhlAn3 to identify the population ascribed to the class Clostridia. Intestinal Clostridia genomes were retrieved and subjected to AAI analysis and core genome identification. Phylogeny investigation was conducted with RAxML and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) algorithms, and SplitsTree for split decomposition. Results: 225 out of 406 bacterial taxonomic units were ascribed to Bacillota [Firmicutes], among which 124 were assigned to the class Clostridia. 77 out of the 124 taxonomic units were referred to a species, altogether covering 87.7% of Clostridia abundance. According to the lowest AAI genus boundary set at 55%, 15 putative genera encompassing more than one species (G1 to G15) were identified, while 19 species did not cluster with any other one and each appeared to belong to a diverse genus. Phylogenetic investigations highlighted that most of the species clustered into three main evolutive clades. Conclusion: This study shed light on the species of Clostridia colonizing the gut of healthy adults and pinpointed several gaps in knowledge regarding the taxonomy and the phylogeny of Clostridia.}, }
@article {pmid38047277, year = {2023}, author = {Shetty, SA and Kool, J and Fuentes, S}, title = {A tool to assess the mock community samples in 16S rRNA gene-based microbiota profiling studies.}, journal = {Microbiome research reports}, volume = {2}, number = {2}, pages = {14}, pmid = {38047277}, issn = {2771-5965}, abstract = {Inclusion and investigation of technical controls in microbiome sequencing studies is important for understanding technical biases and errors. Here, we present chkMocks, a general R-based tool that allows researchers to compare the composition of mock communities that are processed along with samples to their theoretical composition. A visual comparison between experimental and theoretical community composition and their correlation is provided for researchers to assess the quality of their sample processing workflows.}, }
@article {pmid38047235, year = {2023}, author = {Fremin, BJ and Bhatt, AS and Kyrpides, NC}, title = {Identification of over ten thousand candidate structured RNAs in viruses and phages.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {5630-5639}, pmid = {38047235}, issn = {2001-0370}, abstract = {Structured RNAs play crucial roles in viruses, exerting influence over both viral and host gene expression. However, the extensive diversity of structured RNAs and their ability to act in cis or trans positions pose challenges for predicting and assigning their functions. While comparative genomics approaches have successfully predicted candidate structured RNAs in microbes on a large scale, similar efforts for viruses have been lacking. In this study, we screened over 5 million DNA and RNA viral sequences, resulting in the prediction of 10,006 novel candidate structured RNAs. These predictions are widely distributed across taxonomy and ecosystem. We found transcriptional evidence for 206 of these candidate structured RNAs in the human fecal microbiome. These candidate RNAs exhibited evidence of nucleotide covariation, indicative of selective pressure maintaining the predicted secondary structures. Our analysis revealed a diverse repertoire of candidate structured RNAs, encompassing a substantial number of putative tRNAs or tRNA-like structures, Rho-independent transcription terminators, and potentially cis-regulatory structures consistently positioned upstream of genes. In summary, our findings shed light on the extensive diversity of structured RNAs in viruses, offering a valuable resource for further investigations into their functional roles and implications in viral gene expression and pave the way for a deeper understanding of the intricate interplay between viruses and their hosts at the molecular level.}, }
@article {pmid38047079, year = {2023}, author = {Galaz, J and Romero, R and Greenberg, JM and Theis, KR and Arenas-Hernandez, M and Xu, Y and Farias-Jofre, M and Miller, D and Kanninen, T and Garcia-Flores, V and Gomez-Lopez, N}, title = {Host-microbiome interactions in distinct subsets of preterm labor and birth.}, journal = {iScience}, volume = {26}, number = {12}, pages = {108341}, pmid = {38047079}, issn = {2589-0042}, abstract = {Preterm birth, the leading cause of perinatal morbidity, often follows premature labor, a syndrome whose prevention remains a challenge. To better understand the relationship between premature labor and host-microbiome interactions, we conducted a mechanistic investigation using three preterm birth models. We report that intra-amniotic delivery of LPS triggers inflammatory responses in the amniotic cavity and cervico-vaginal microenvironment, causing vaginal microbiome changes and signs of active labor. Intra-amniotic IL-1α delivery causes a moderate inflammatory response in the amniotic cavity but increasing inflammation in the cervico-vaginal space, leading to vaginal microbiome disruption and signs of active labor. Conversely, progesterone action blockade by RU-486 triggers local immune responses accompanying signs of active labor without altering the vaginal microbiome. Preterm labor facilitates ascension of cervico-vaginal bacteria into the amniotic cavity, regardless of stimulus. This study provides compelling mechanistic insights into the dynamic host-microbiome interactions within the cervico-vaginal microenvironment that accompany premature labor and birth.}, }
@article {pmid38046824, year = {2023}, author = {Procaccianti, G and Roggiani, S and Conti, G and Brigidi, P and Turroni, S and D'Amico, F}, title = {Bifidobacterium in anticancer immunochemotherapy: friend or foe?.}, journal = {Microbiome research reports}, volume = {2}, number = {3}, pages = {24}, pmid = {38046824}, issn = {2771-5965}, abstract = {The gut microbiome has received a crescendo of attention in recent years due to myriad influences on human pathophysiology, including cancer. Anticancer therapy research is constantly looking for new hints to improve response to therapy while reducing the risk of relapse. In this scenario, Bifidobacterium, which inhabits the gut microbial ecosystem (especially that of children) and is considered a health-associated microbe, has emerged as a key target to assist anticancer treatments for a better prognosis. However, some researchers have recently hypothesized an unfavorable role of Bifidobacterium spp. in anticancer immunochemotherapy, leading to some confusion in the field. This narrative review summarizes the current knowledge on the role of Bifidobacterium spp. in relation to anticancer treatments, discussing the pros and cons of its presence in the gut microbiome of cancer patients. The current intervention strategies based on the administration of probiotic strains of Bifidobacterium are then discussed. Finally, the need to conduct further studies, especially functional ones, is underlined to provide robust experimental evidence, especially on the underlying molecular mechanisms, and thus resolve the controversies on this microbe for the long-term success of immunochemotherapy.}, }
@article {pmid38046822, year = {2023}, author = {Martin, AJM and Serebrinsky-Duek, K and Riquelme, E and Saa, PA and Garrido, D}, title = {Microbial interactions and the homeostasis of the gut microbiome: the role of Bifidobacterium.}, journal = {Microbiome research reports}, volume = {2}, number = {3}, pages = {17}, pmid = {38046822}, issn = {2771-5965}, abstract = {The human gut is home to trillions of microorganisms that influence several aspects of our health. This dense microbial community targets almost all dietary polysaccharides and releases multiple metabolites, some of which have physiological effects on the host. A healthy equilibrium between members of the gut microbiota, its microbial diversity, and their metabolites is required for intestinal health, promoting regulatory or anti-inflammatory immune responses. In contrast, the loss of this equilibrium due to antibiotics, low fiber intake, or other conditions results in alterations in gut microbiota composition, a term known as gut dysbiosis. This dysbiosis can be characterized by a reduction in health-associated microorganisms, such as butyrate-producing bacteria, enrichment of a small number of opportunistic pathogens, or a reduction in microbial diversity. Bifidobacterium species are key species in the gut microbiome, serving as primary degraders and contributing to a balanced gut environment in various ways. Colonization resistance is a fundamental property of gut microbiota for the prevention and control of infections. This community competes strongly with foreign microorganisms, such as gastrointestinal pathogens, antibiotic-resistant bacteria, or even probiotics. Resistance to colonization is based on microbial interactions such as metabolic cross-feeding, competition for nutrients, or antimicrobial-based inhibition. These interactions are mediated by metabolites and metabolic pathways, representing the inner workings of the gut microbiota, and play a protective role through colonization resistance. This review presents a rationale for how microbial interactions provide resistance to colonization and gut dysbiosis, highlighting the protective role of Bifidobacterium species.}, }
@article {pmid38046821, year = {2023}, author = {Mancabelli, L and Milani, C and Fontana, F and Liotto, N and Tabasso, C and Perrone, M and Lugli, GA and Tarracchini, C and Alessandri, G and Viappiani, A and Bernasconi, S and Roggero, P and Mosca, F and Turroni, F and Ventura, M}, title = {A pilot study to disentangle the infant gut microbiota composition and identification of bacteria correlates with high fat mass.}, journal = {Microbiome research reports}, volume = {2}, number = {3}, pages = {23}, pmid = {38046821}, issn = {2771-5965}, abstract = {Background: At birth, the human intestine is colonized by a complex community of microorganisms known as gut microbiota. These complex microbial communities that inhabit the gut microbiota are thought to play a key role in maintaining host physiological homeostasis. For this reason, correct colonization of the gastrointestinal tract in the early stages of life could be fundamental for human health. Furthermore, alterations of the infant microbiota are correlated with the development of human inflammatory diseases and disorders. In this context, the possible relationships between intestinal microbiota and body composition during infancy are of great interest. Methods: In this study, we have performed a pilot study based on 16S rRNA gene profiling and metagenomic approaches on repeatedly measured data on time involving a cohort of 41 Italian newborns, which is aimed to investigate the possible correlation between body fat mass percentage (FM%) and the infant gut microbiota composition. Results and conclusion: The taxonomical analysis of the stool microbiota of each infant included in the cohort allowed the identification of a specific correlation between intestinal bacteria, such as Bifidobacterium and Veillonella, and the increase in FM%. Moreover, the analysis of the infant microbiome's metabolic capabilities suggested that the intestinal microbiome functionally impacts the human host and its possible influence on host physiology.}, }
@article {pmid38046820, year = {2023}, author = {Roggiani, S and Mengoli, M and Conti, G and Fabbrini, M and Brigidi, P and Barone, M and D'Amico, F and Turroni, S}, title = {Gut microbiota resilience and recovery after anticancer chemotherapy.}, journal = {Microbiome research reports}, volume = {2}, number = {3}, pages = {16}, pmid = {38046820}, issn = {2771-5965}, abstract = {Although research on the role of the gut microbiota (GM) in human health has sharply increased in recent years, what a "healthy" gut microbiota is and how it responds to major stressors is still difficult to establish. In particular, anticancer chemotherapy is known to have a drastic impact on the microbiota structure, potentially hampering its recovery with serious long-term consequences for patients' health. However, the distinguishing features of gut microbiota recovery and non-recovery processes are not yet known. In this narrative review, we first investigated how gut microbiota layouts are affected by anticancer chemotherapy and identified potential gut microbial recovery signatures. Then, we discussed microbiome-based intervention strategies aimed at promoting resilience, i.e., the rapid and complete recovery of a healthy gut microbial network associated with a better prognosis after such high-impact pharmacological treatments.}, }
@article {pmid38046818, year = {2023}, author = {Sane, F and Piva, F and Romond, MB}, title = {Free lipoproteins from Bifidobacterium longum alleviate osteoarthritis through modulation of the gut microbiome.}, journal = {Microbiome research reports}, volume = {2}, number = {3}, pages = {18}, pmid = {38046818}, issn = {2771-5965}, abstract = {Aim: The "gut-joint" axis is suspected to be involved in the pathophysiology of osteoarthritis (OA). The present study aims at investigating the potential of lipoproteins (Lpps) secreted by Bifidobacterium longum to alleviate OA progression in the rat. Methods: Experimental OA was induced in rats harbouring Schaedler Flora maintained in SPF conditions. Two weeks post-injection, 20 rats were randomized to water (n = 10) or 0.3 mg/L Lpps solution (n = 10). Weight and food intake were monitored for 6 weeks. At sacrifice, joints were scored using macroscopic and histological criteria. Serum LPS, Schaedler flora as well as selected intestinal bacteria were analyzed. Results: Lpps intake prevents OA progression. The protected rats showed a significant increase in lactobacilli along the intestine as well as in Mucispirillum schaedleri in the colon and a significant decrease in Parabacteroides goldsteini and Akkermansia in caecum and colon, respectively. There was no significant difference in serum lipopolysaccharide or bacteria translocating in Peyer's patches. Labelled Lpps were not detected in bone marrow of the OA joint. The principal component analysis points out that OA prevention is primarily associated with bacteria involved in the tryptophane degradation pathway and SCFA formation. Conclusion: In rats deprived of bifidobacteria, intake of B.longum Lpps prevented OA development and modulated the intestinal microbiome with a possible impact on the bacterial end-products. The link between Lpps and the gut microbial metabolome warrants further investigation.}, }
@article {pmid38046097, year = {2023}, author = {Oliver, A and Kay, M and Lemay, DG}, title = {TaxaHFE: a machine learning approach to collapse microbiome datasets using taxonomic structure.}, journal = {Bioinformatics advances}, volume = {3}, number = {1}, pages = {vbad165}, pmid = {38046097}, issn = {2635-0041}, abstract = {MOTIVATION: Biologists increasingly turn to machine learning models not just to predict, but to explain. Feature reduction is a common approach to improve both the performance and interpretability of models. However, some biological datasets, such as microbiome data, are inherently organized in a taxonomy, but these hierarchical relationships are not leveraged during feature reduction. We sought to design a feature engineering algorithm to exploit relationships in hierarchically organized biological data.<br><br>RESULTS: We designed an algorithm, called TaxaHFE, to collapse information-poor features into their higher taxonomic levels. We applied TaxaHFE to six previously published datasets and found, on average, a 90% reduction in the number of features (SD&#x2009;=&#x2009;5.1%) compared to using the most complete taxonomy. Using machine learning to compare the most resolved taxonomic level (i.e. species) against TaxaHFE-preprocessed features, models based on TaxaHFE features achieved an average increase of 3.47% in receiver operator curve area under the curve. Compared to other hierarchical feature engineering implementations, TaxaHFE introduces the novel ability to consider both categorical and continuous response variables to inform the feature set collapse. Importantly, we find TaxaHFE's ability to reduce hierarchically organized features to a more information-rich subset increases the interpretability of models.<br><br>TaxaHFE is available as a Docker image and as R code at https://github.com/aoliver44/taxaHFE.}, }
@article {pmid38046046, year = {2023}, author = {Ahmad, S and Sands, M and Greenberg, E and Tangen, L and Huang, J and Irudayaraj, JMK}, title = {Mucosal DNA methylome alteration in Crohn's disease: surgical and non-surgical groups.}, journal = {Frontiers in genetics}, volume = {14}, number = {}, pages = {1244513}, pmid = {38046046}, issn = {1664-8021}, abstract = {Crohn's disease (CD) is characterized as a chronic, relapsing, and progressive disorder with a complex etiology involving interactions between host, microbiome, and the external environment. Genome wide association studies (GWAS) suggest several genetic variations in the diseased individuals but that explains only a small proportion of susceptibility to disease conditions. This indicates the possible role of epigenome which links environmental factors to the genetic variation in the disease etiology. The current study is focused on the DNA methylome evolution with disease progression. We performed Reduced Representation Bisulfite Sequencing (RRBS) to analyze differential DNA methylation in the diseased and healthy mucosal tissues of 2 different groups of CD patients: non-surgical and surgical, categorized based on the severity of disease and standard of care needed. Patients in both groups have unique DNA methylation signature compared to the healthy tissue. After removing single nucleotide polymorphisms (SNPs), 1,671 differentially methylated loci were found in the non-surgical and 3,334 in the surgical group of which only 206 were found overlapping in both groups. Furthermore, differential DNA methylation was noted in some of the GWAS associated genes implicated in CD. Also, functional enrichment analysis showed high representation of several key pathways where differential methylations were observed, and these can be implicated in CD pathogenesis. We identified specific DNA methylation patterns in the mucosal DNA of surgical and non-surgical CD patients which indicates evolution of the methylome as the disease progresses from initial to the advance stage. These unique patterns can be used as DNA methylation signatures to identify different stages of the disease.}, }
@article {pmid38045924, year = {2023}, author = {Mengoli, M and Conti, G and Fabbrini, M and Candela, M and Brigidi, P and Turroni, S and Barone, M}, title = {Microbiota-gut-brain axis and ketogenic diet: how close are we to tackling epilepsy?.}, journal = {Microbiome research reports}, volume = {2}, number = {4}, pages = {32}, pmid = {38045924}, issn = {2771-5965}, abstract = {The microbiota-gut-brain axis refers to the intricate bidirectional communication between commensal microorganisms residing in the digestive tract and the central nervous system, along neuroendocrine, metabolic, immune, and inflammatory pathways. This axis has been suggested to play a role in several neurological disorders, such as Parkinson's disease, Alzheimer's disease, multiple sclerosis, and epilepsy, paving the way for microbiome-based intervention strategies for the mitigation and treatment of symptoms. Epilepsy is a multifaceted neurological condition affecting more than 50 million individuals worldwide, 30% of whom do not respond to conventional pharmacological therapies. Among the first-hand microbiota modulation strategies, nutritional interventions represent an easily applicable option in both clinical and home settings. In this narrative review, we summarize the mechanisms underlying the microbiota-gut-brain axis involvement in epilepsy, discuss the impact of antiepileptic drugs on the gut microbiome, and then the impact of a particular dietary pattern, the ketogenic diet, on the microbiota-gut-brain axis in epileptic patients. The investigation of the microbiota response to non-pharmacological therapies is an ever-expanding field with the potential to allow the design of increasingly accessible and successful intervention strategies.}, }
@article {pmid38045923, year = {2023}, author = {Al, KF and Allen, L and Bedell, S and Burton, JP and de Vrijer, B}, title = {Assessing the impact of pregnancy and birth factors on the maternal and infant microbiota.}, journal = {Microbiome research reports}, volume = {2}, number = {4}, pages = {29}, pmid = {38045923}, issn = {2771-5965}, abstract = {Background: The microbiota acquired at birth is known to play an intimate role in later life health and disease and has been shown to be affected by the mode of birth. There has been recent interest in microbiota correction by maternal vaginal seeding in Cesarean section-born infants; however, the safety of this practice has been debated. The aim of this study was to assess how other factors, such as timing of sampling, maternal obesity, vaginal Group B Streptococcus colonization (GBS), and antibiotic exposure, affect the maternal and infant microbiota. Methods: Maternal vaginal and saliva samples were collected at three time periods: 35-37 weeks gestation (prenatal), within 24-36 hours after birth (birth), and at ~6 weeks postpartum. Infant saliva and stool samples were collected at ~6 weeks postpartum. 16S rRNA amplicon sequencing was utilized to assess the taxonomic and inferred functional compositions of the bacterial communities from both mothers and infants. Results: Samples from 36 mothers and 32 infants were obtained. Gestational age, breastfeeding, mode of birth, and gravidity were associated with taxonomic alterations in the infant samples, while obesity, antibiotic use, and GBS status were not. Maternal samples were predominantly affected by time, whereby significant alterations including increased microbial diversity were seen at birth and persisted to 6 weeks postpartum. Conclusion: This study provides information on the relationship between health and delivery factors and changes in vaginal and infant microbiota. These results may better direct clinicians and mothers in optimizing the infant microbiota towards health during infancy and later life.}, }
@article {pmid38045684, year = {2023}, author = {Munjoma, PT and Chandiwana, P and Wyss, J and Mazhandu, AJ and Jordi, SBU and Gutsire, R and Katsidzira, L and Yilmaz, B and Misselwitz, B and Duri, K}, title = {Immune activation and inflammation in lactating women on combination antiretroviral therapy: role of gut dysfunction and gut microbiota imbalance.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1280262}, pmid = {38045684}, issn = {1664-3224}, mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Antiretroviral Therapy, Highly Active ; Lipopolysaccharide Receptors ; Lactation ; *HIV Infections/drug therapy ; Zimbabwe ; Inflammation/drug therapy ; Biomarkers ; Leukocyte L1 Antigen Complex ; }, abstract = {INTRODUCTION: Combination antiretroviral therapy (cART) effectively controls HIV; however, chronic low-level viremia and gut microbiota dysbiosis remain significant drivers of gut and systemic inflammation. In this study, we explored the relationship between gut microbiota composition, intestinal inflammation, microbial translocation, and systemic inflammation in women on cART in Sub-Saharan Africa.<br><br>METHODS: We conducted a study in HIV-infected and HIV-uninfected lactating women followed up at 6 weeks and 6 months postpartum in Harare, Zimbabwe. We used 16S ribosomal Ribonucleic Acid (rRNA) sequencing and MesoScale Discovery V-Plex assays to examine the gut microbiome and to quantify plasma inflammatory biomarkers, respectively. In addition, we measured fecal calprotectin, plasma lipopolysaccharide-binding protein (LBP), and soluble cluster of differentiation 14 (sCD14) by enzyme-linked immunosorbent assay to assess gut inflammation, microbial translocation, and monocyte/macrophage activation.<br><br>RESULTS: A group of 77 lactating women were studied, of which 35% were HIV-infected. Fecal calprotectin levels were similar by HIV status at both follow-up time points. In the HIV-infected group at 6 weeks postpartum, fecal calprotectin was elevated: median (interquartile range) [158.1 &#xb5;g/g (75.3-230.2)] in women who had CD4+ T-lymphocyte counts <350 cells/&#xb5;L compared with those with &#x2265;350 cells/&#xb5;L [21.1 &#xb5;g/g (0-58.4)], p = 0.032. Plasma sCD14 levels were significantly higher in the HIV-infected group at both 6 weeks and 6 months postpartum, p < 0.001. Plasma LBP levels were similar, but higher levels were observed in HIV-infected women with elevated fecal calprotectin. We found significant correlations between fecal calprotectin, LBP, and sCD14 with proinflammatory cytokines. Gut microbial alpha diversity was not affected by HIV status and was not affected by use of antibiotic prophylaxis. HIV significantly affected microbial beta diversity, and significant differences in microbial composition were noted. The genera Slackia and Collinsella were relatively more abundant in the HIV-infected group, whereas a lower relative abundance of Clostriduim sensu_stricto_1 was observed. Our study also found correlations between gut microbial taxa abundance and systemic inflammatory biomarkers.<br><br>DISCUSSION AND CONCLUSION: HIV-infected lactating women had increased immune activation and increased microbial translocation associated with increased gut inflammation. We identified correlations between the gut inflammation and microbial composition, microbial translocation, and systemic inflammation. The interplay of these parameters might affect the health of this vulnerable population.}, }
@article {pmid38046907, year = {2022}, author = {Ventura, M and van Sinderen, D and Turroni, F}, title = {New research frontiers pertaining to the infant gut microbiota.}, journal = {Microbiome research reports}, volume = {1}, number = {4}, pages = {24}, pmid = {38046907}, issn = {2771-5965}, abstract = {The human gut microbiota is believed to be responsible for multiple health-impacting host effects. The influence of gut microorganisms on the human host begins immediately after birth, having long-lasting health effects, while the gut microbiota itself continues to develop throughout the host's entire life. The purported health-associated effects of the gut microbiota have fueled extensive and ongoing research efforts. Nonetheless, the precise mode of action of functionalities exerted by microbial colonizers of the infant intestine is still largely unknown. The current perspective intends to illustrate major future investigative directions concerning the human gut microbiota with a specific focus on infant-associated gut microbes.}, }
@article {pmid38046360, year = {2022}, author = {Sanozky-Dawes, R and Barrangou, R}, title = {Lactobacillus, glycans and drivers of health in the vaginal microbiome.}, journal = {Microbiome research reports}, volume = {1}, number = {3}, pages = {18}, pmid = {38046360}, issn = {2771-5965}, abstract = {A microbiome consists of microbes and their genomes, encompassing bacteria, viruses, fungi, protozoa, archaea, and eukaryotes. These elements interact dynamically in the specific environment in which they reside and evolve. In the past decade, studies of various microbiomes have been prevalent in the scientific literature, accounting for the shift from culture-dependent to culture-independent identification of microbes using new high-throughput sequencing technologies that decipher their composition and sometimes provide insights into their functions. Despite tremendous advances in understanding the gut microbiome, relatively little attention has been devoted to the vaginal environment, notably regarding the ubiquity and diversity of glycans which denote the significant role they play in the maintenance of homeostasis. Hopefully, emerging technologies will aid in the determination of what is a healthy vaginal microbiome, and provide insights into the roles of Lactobacillus, glycans and microbiome-related drivers of health and disease.}, }
@article {pmid38046357, year = {2022}, author = {Aguanno, D and Metwaly, A and Coleman, OI and Haller, D}, title = {Modeling microbiota-associated human diseases: from minimal models to complex systems.}, journal = {Microbiome research reports}, volume = {1}, number = {3}, pages = {17}, pmid = {38046357}, issn = {2771-5965}, abstract = {Alterations in the intestinal microbiota are associated with various human diseases of the digestive system, including obesity and its associated metabolic diseases, inflammatory bowel diseases (IBD), and colorectal cancer (CRC). All three diseases are characterized by modifications of the richness, composition, and metabolic functions of the human intestinal microbiota. Despite being multi-factorial diseases, studies in germ-free animal models have unarguably identified the intestinal microbiota as a causal driver of disease pathogenesis. However, for an increased mechanistic understanding of microbial signatures in human diseases, models require detailed refinement to closely mimic the human microbiota and reflect the complexity and range of dysbiosis observed in patients. The transplantation of human fecal microbiota into animal models represents a powerful tool for studying the causal and functional role of the dysbiotic human microbiome in a pathological context. While human microbiota-associated models were initially employed to study obesity, an increasing number of studies have applied this approach in the context of IBD and CRC over the past decade. In this review, we discuss different approaches that allow the functional validation of the bacterial contribution to human diseases, with emphasis on obesity and its associated metabolic diseases, IBD, and CRC. We discuss the utility of simple models, such as in vitro fermentation systems of the human microbiota and ex vivo intestinal organoids, as well as more complex whole organism models. Our focus here lies on human microbiota-associated mouse models in the context of all three diseases, as well as highlighting the advantages and limitations of this approach.}, }
@article {pmid38046361, year = {2022}, author = {Narduzzi, L and Agulló, V and Favari, C and Tosi, N and Mignogna, C and Crozier, A and Rio, DD and Mena, P}, title = {(Poly)phenolic compounds and gut microbiome: new opportunities for personalized nutrition.}, journal = {Microbiome research reports}, volume = {1}, number = {3}, pages = {16}, pmid = {38046361}, issn = {2771-5965}, abstract = {For decades, (poly)phenols have been linked to cardiometabolic health, but population heterogeneity limits their apparent efficacy and the development of tailored, practical protocols in dietary interventions. This heterogeneity is likely determined by the existence of different metabotypes, sub-populations of individuals metabolizing some classes of (poly)phenols differently. The gut microbiota plays a major role in this process. The impact of microbiota-related phenolic metabotypes on cardiometabolic health is becoming evident, although the picture is still incomplete, and data are absent for some classes of (poly)phenols. The lack of a complete understanding of the main microbial actors involved in the process complicates the picture. Elucidation of the mechanisms behind phenolic metabotypes requires novel experimental designs that can dissect the inter-individual variability. This paper, in addition to providing an overview on the current state-of-the-art, proposes wider metabotyping approaches as a means of paving the way towards effective personalized nutrition with dietary (poly)phenols.}, }
@article {pmid38045644, year = {2022}, author = {Strain, R and Stanton, C and Ross, RP}, title = {Effect of diet on pathogen performance in the microbiome.}, journal = {Microbiome research reports}, volume = {1}, number = {2}, pages = {13}, pmid = {38045644}, issn = {2771-5965}, abstract = {Intricate interactions among commensal bacteria, dietary substrates and immune responses are central to defining microbiome community composition, which plays a key role in preventing enteric pathogen infection, a dynamic phenomenon referred to as colonisation resistance. However, the impact of diet on sculpting microbiota membership, and ultimately colonisation resistance has been overlooked. Furthermore, pathogens have evolved strategies to evade colonisation resistance and outcompete commensal microbiota by using unique nutrient utilisation pathways, by exploiting microbial metabolites as nutrient sources or by environmental cues to induce virulence gene expression. In this review, we will discuss the interplay between diet, microbiota and their associated metabolites, and how these can contribute to or preclude pathogen survival.}, }
@article {pmid38045649, year = {2022}, author = {Linehan, K and Dempsey, EM and Ryan, CA and Ross, RP and Stanton, C}, title = {First encounters of the microbial kind: perinatal factors direct infant gut microbiome establishment.}, journal = {Microbiome research reports}, volume = {1}, number = {2}, pages = {10}, pmid = {38045649}, issn = {2771-5965}, abstract = {The human gut microbiome harbors a diverse range of microbes that play a fundamental role in the health and well-being of their host. The early-life microbiome has a major influence on human development and long-term health. Perinatal factors such as maternal nutrition, antibiotic use, gestational age and mode of delivery influence the initial colonization, development, and function of the neonatal gut microbiome. The perturbed early-life gut microbiome predisposes infants to diseases in early and later life. Understanding how perinatal factors guide and shape the composition of the early-life microbiome is essential to improving infant health. The following review provides a synopsis of perinatal factors with the most decisive influences on initial microbial colonization of the infant gut.}, }
@article {pmid38045646, year = {2022}, author = {Lugli, GA and Ventura, M}, title = {A breath of fresh air in microbiome science: shallow shotgun metagenomics for a reliable disentangling of microbial ecosystems.}, journal = {Microbiome research reports}, volume = {1}, number = {2}, pages = {8}, pmid = {38045646}, issn = {2771-5965}, abstract = {Next-generation sequencing technologies allow accomplishing massive DNA sequencing, uncovering the microbial composition of many different ecological niches. However, the various strategies developed to profile microbiomes make it challenging to retrieve a reliable classification that is able to compare metagenomic data of different studies. Many limitations have been overcome thanks to shotgun sequencing, allowing a reliable taxonomic classification of microbial communities at the species level. Since numerous bioinformatic tools and databases have been implemented, the sequencing methodology is only the first of many choices to make for classifying metagenomic data. Here, we discuss the importance of choosing a reliable methodology to achieve consistent information in uncovering microbiomes.}, }
@article {pmid38045612, year = {2023}, author = {Brüssow, H}, title = {The human microbiome project at ten years - some critical comments and reflections on "our third genome", the human virome.}, journal = {Microbiome research reports}, volume = {2}, number = {1}, pages = {7}, pmid = {38045612}, issn = {2771-5965}, abstract = {The Human Microbiome Project (HMP) has raised great expectations claiming the far-reaching influence of the microbiome on human health and disease ranging from obesity and malnutrition to effects going well beyond the gut. So far, with the notable exception of fecal microbiota transplantation in Clostridioides difficile infection, practical application of microbiome intervention has only achieved modest clinical effects. It is argued here that we need criteria for the link between microbiome and disease modelled on the links between pathogens and infectious disease in Koch's postulates. The most important question is whether the microbiome change is a cause of the given disease or a consequence of a pathology leading to disease where the microbiome change is only a parallel event without a causal connection to the disease - in philosophical parlance, an epiphenomenon. Also discussed here is whether human virome research is a necessary complement to the microbiome project with a high potential for practical applications.}, }
@article {pmid38045609, year = {2023}, author = {Sabater, C and Iglesias-Gutiérrez, E and Ruiz, L and Margolles, A}, title = {Next-generation sequencing of the athletic gut microbiota: a systematic review.}, journal = {Microbiome research reports}, volume = {2}, number = {1}, pages = {5}, pmid = {38045609}, issn = {2771-5965}, abstract = {Aim: There is growing evidence that physical activity modulates gut microbiota composition through complex interactions between diet and microbial species. On the other hand, next-generation sequencing techniques include shotgun metagenomics and 16S amplicon sequencing. These methodologies allow a comprehensive characterisation of microbial communities of athletes from different disciplines as well as non-professional players and sedentary adults exposed to training. This systematic review summarises recent applications of next-generation sequencing to characterise the athletic gut microbiome. Methods: A systematic review of microbiome research was performed to determine the association of microbiota composition profiles with sports performance. Results: Bibliographic analysis revealed the importance of a novel research trend aiming at deciphering the associations between individual microbial species and sports performance. In addition, literature review highlighted the role of butyrate-producing bacteria such as Anaerostipes hadrus, Clostridium bolteae, Faecalibacterium prausnitzii, Roseburia hominis and unidentified species belonging to Clostridiales, Lachnospiraceae and Subdoligranulum species in gut health and sports performance across several disciplines. Interestingly, metabolic activities of Prevotella copri and Veillonella atypica involved in branched amino acid and lactate metabolism may contribute to reducing muscular fatigue. Other microbial metabolic pathways of interest involved in carbohydrate metabolism showed increased proportions in athletes´ metagenomes. Conclusion: Future research will aim at developing personalised nutrition interventions to modulate key species associated with certain components of exercise.}, }
@article {pmid38045412, year = {2023}, author = {Lind, AL and McDonald, NA and Gerrick, ER and Bhatt, AS and Pollard, KS}, title = {Hybrid assemblies of microbiome Blastocystis protists reveal evolutionary diversification reflecting host ecology.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.11.20.567959}, pmid = {38045412}, abstract = {The most prevalent microbial eukaryote in the human gut is Blastocystis , an obligate commensal protist also common in many other vertebrates. Blastocystis is descended from free-living stramenopile ancestors; how it has adapted to thrive within humans and a wide range of hosts is unclear. Here, we cultivated six Blastocystis strains spanning the diversity of the genus and generated highly contiguous, annotated genomes with long-read DNA-seq, Hi-C, and RNA-seq. Comparative genomics between these strains and two closely related stramenopiles with different lifestyles, the lizard gut symbiont Proteromonas lacertae and the free-living marine flagellate Cafeteria burkhardae , reveal the evolutionary history of the Blastocystis genus. We find substantial gene content variability between Blastocystis strains. Blastocystis isolated from an herbivorous tortoise has many plant carbohydrate metabolizing enzymes, some horizontally acquired from bacteria, likely reflecting fermentation within the host gut. In contrast, human- isolated Blastocystis have gained many heat shock proteins, and we find numerous subtype- specific expansions of host-interfacing genes, including cell adhesion and cell surface glycan genes. In addition, we observe that human-isolated Blastocystis have substantial changes in gene structure, including shortened introns and intergenic regions, as well as genes lacking canonical termination codons. Finally, our data indicate that the common ancestor of Blastocystis lost nearly all ancestral genes for heterokont flagella morphology, including cilia proteins, microtubule motor proteins, and ion channel proteins. Together, these findings underscore the huge functional variability within the Blastocystis genus and provide candidate genes for the adaptations these lineages have undergone to thrive in the gut microbiomes of diverse vertebrates.}, }
@article {pmid38045399, year = {2023}, author = {Olm, MR and Spencer, SP and Silva, EL and Sonnenburg, JL}, title = {Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.11.21.568153}, pmid = {38045399}, abstract = {IgA, the most highly produced human antibody, is continually secreted into the gut to shape the intestinal microbiota. Methodological limitations have critically hindered defining which microbial strains are targeted by IgA and why. Here, we develop a new technique, Metagenomic Immunoglobulin Sequencing (MIG-Seq), and use it to determine IgA coating levels for thousands of gut microbiome strains in healthy humans. We find that microbes associated with both health and disease have higher levels of coating, and that microbial genes are highly predictive of IgA binding levels, with mucus degradation genes especially correlated with high binding. We find a significant reduction in replication rates among microbes bound by IgA, and demonstrate that IgA binding is more correlated with host immune status than traditional microbial abundance measures. This study introduces a powerful technique for assessing strain-level IgA binding in human stool, paving the way for deeper understanding of IgA-based host microbe interactions.}, }
@article {pmid38045370, year = {2023}, author = {Do, K and Mehta, S and Wagner, R and Bhuming, D and Rajczewski, AT and Skubitz, APN and Johnson, JE and Griffin, TJ and Jagtap, PD}, title = {A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.11.21.568121}, pmid = {38045370}, abstract = {Clinical metaproteomics has the potential to offer insights into the host-microbiome interactions underlying diseases. However, the field faces challenges in characterizing microbial proteins found in clinical samples, which are usually present at low abundance relative to the host proteins. As a solution, we have developed an integrated workflow coupling mass spectrometry-based analysis with customized bioinformatic identification, quantification and prioritization of microbial and host proteins, enabling targeted assay development to investigate host-microbe dynamics in disease. The bioinformatics tools are implemented in the Galaxy ecosystem, offering the development and dissemination of complex bioinformatic workflows. The modular workflow integrates MetaNovo (to generate a reduced protein database), SearchGUI/PeptideShaker and MaxQuant (to generate peptide-spectral matches (PSMs) and quantification), PepQuery2 (to verify the quality of PSMs), and Unipept and MSstatsTMT (for taxonomy and functional annotation). We have utilized this workflow in diverse clinical samples, from the characterization of nasopharyngeal swab samples to bronchoalveolar lavage fluid. Here, we demonstrate its effectiveness via analysis of residual fluid from cervical swabs. The complete workflow, including training data and documentation, is available via the Galaxy Training Network, empowering non-expert researchers to utilize these powerful tools in their clinical studies.}, }
@article {pmid38045337, year = {2023}, author = {Wang, T and Fu, Y and Shuai, M and Zheng, JS and Zhu, L and Sun, Q and Hu, FB and Weiss, ST and Liu, YY}, title = {Microbiome-based correction of nutrient profiles derived from self-reported dietary assessments.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.11.21.568102}, pmid = {38045337}, abstract = {Since dietary intake is hard to directly measure in large-scale cohort studies, we often rely on self-reported instruments (e.g., food frequency questionnaires, diet recall surveys, and diet diary methods) developed in nutritional epidemiology. Those self-reported instruments are prone to measurement errors. The measurement errors eventually lead to inaccuracies in the calculation of nutrient profiles. Currently, there is a lack of computational methods to address this problem. To fill the gap, we introduce a deep-learning approach --- M icrobiom e -based nu t rient p r of i le c orrector (METRIC), which leverages gut microbial compositions to correct the errors in nutrient profiles due to measurement errors in self-reported dietary assessments. We demonstrate the excellent performance of METRIC in minimizing the simulated random errors in both synthetic and three real-world datasets. METRIC has the potential to significantly improve the accuracy of self-reported dietary assessments and hence facilitate the research of nutritional epidemiology.}, }
@article {pmid38045323, year = {2023}, author = {Mudbhari, S and Lofgren, L and Appidi, MR and Vilgalys, R and Hettich, RL and Abraham, P}, title = {Decoding the chemical language of Suillus fungi: genome mining and untargeted metabolomics uncover terpene chemical diversity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.11.20.567897}, pmid = {38045323}, abstract = {UNLABELLED: Ectomycorrhizal fungi establish mutually beneficial relationships with trees, trading nutrients for carbon. Suillus are ectomycorrhizal fungi that are critical to the health of boreal and temperate forest ecosystems. Comparative genomics has identified a high number of non-ribosomal peptide synthetase and terpene biosynthetic gene clusters (BGC) potentially involved in fungal competition and communication. However, the functionality of these BGCs is not known. This study employed co-culture techniques to activate BGC expression and then used metabolomics to investigate the diversity of metabolic products produced by three Suillus species (S. hirtellus EM16, S. decipiens EM49, and S. cothurnatus VC1858), core members of the Pine microbiome. After 28 days of growth on solid media, liquid chromatography-tandem mass spectrometry identified a diverse range of extracellular metabolites (exometabolites) along the interaction zone between Suillus co-cultures. Prenol lipids were among the most abundant chemical classes. Out of the 62 unique terpene BGCs predicted by genome mining, 116 putative terpenes were identified across the three Suillus species using metabolomics. Notably, some terpenes were significantly more abundant in co-culture conditions. For example, we identified a metabolite matching to isomers isopimaric acid, sandaracopimaric acid, and abietic acid, which can be found in pine resin and play important roles in host defense mechanisms and Suillus spore germination. This research highlights the importance of combining genomics and metabolomics to advance our understanding of the chemical diversity underpinning fungal signaling and communication.<br><br>IMPORTANCE: Using a combination of genomics and metabolomics, this study's findings offer new insights into the signaling and communication of Suillus fungi, which serve a critical role in forest ecosystems.}, }
@article {pmid38045555, year = {2021}, author = {Turroni, F and van Sinderen, D and Ventura, M}, title = {Bifidobacteria: insights into the biology of a key microbial group of early life gut microbiota.}, journal = {Microbiome research reports}, volume = {1}, number = {1}, pages = {2}, pmid = {38045555}, issn = {2771-5965}, abstract = {The establishment and development of the human gut microbiota constitutes a dynamic and non-random process, which involves positive and negative interactions between key microbial taxa and their host. Remarkably, these early life microbiota-host communications include key events with long-term health consequences. Bifidobacteria arguably represent the most emblematic microbial taxon of the infant gut microbiota. In this context, the interactions among bifidobacteria, their human host, and other members of the human gut microbiota are far from completely understood, despite the crucial role they play in the development and maintenance of human physiology and immune system. Here, we highlight the ecological as well as genetic and functional features of bifidobacteria residing in the human gut using genomic and ecology-based information.}, }
@article {pmid38045253, year = {2023}, author = {Salamzade, R and Kalan, LR}, title = {skDER: microbial genome dereplication approaches for comparative and metagenomic applications.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.09.27.559801}, pmid = {38045253}, abstract = {skDER (https://github.com/raufs/skDER) combines recent advances to efficiently estimate average nucleotide identity (ANI) between thousands of microbial genomes by skani [1] with two low-memory methods for genomic dereplication. The first method implements a dynamic algorithm to determine a concise set of representative genomes. This approach is well-suited for selecting reference genomes to align metagenomic reads onto for tracking strain presence across related microbiome samples. This is because fewer representative genomes should alleviate the concern that reads belonging to the same strain get falsely partitioned across closely related genomes. The other method, which uses a greedy approach, is better suited for use in comparative genomics, where users might be overwhelmed with the high number of genomes available for certain taxa and aim to reduce redundancy and, therefore, computational requirements for downstream analytics. This method selects a larger number of representative genomes to comprehensively sample the pangenome space for the taxon of interest. To further aid usage for comparative genomics studies, skDER also features an option to automatically download genomes classified as a particular species or genus in the Genome Taxonomy Database [2-4] and we provide precomputed representative genomes for commonly studied bacterial taxa [5] .}, }
@article {pmid38045247, year = {2023}, author = {Chatman, CC and Olson, EG and Freedman, AJ and Dittoe, DK and Ricke, SC and Majumder, EL}, title = {Co-exposure to Polyethylene Fiber and Salmonella enterica Typhimurium Alters Microbiome and Metabolome of in vitro Chicken Cecal Mesocosms.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.11.22.568320}, pmid = {38045247}, abstract = {UNLABELLED: Humans and animals encounter a summation of exposures during their lifetime (the exposome). In recent years, the scope of the exposome has begun to include microplastics. Microplastics (MPs) have increasingly been found in locations where there could be an interaction with Salmonella enterica Typhimurium, one of the commonly isolated serovars from processed chicken. In this study, the microbiota response to a 24-hour co-exposure to Salmonella enterica Typhimurium and/or low-density polyethylene (PE) microplastics in an in vitro broiler cecal model was determined using 16S rRNA amplicon sequencing (Illumina) and untargeted metabolomics. Community sequencing results indicated that PE fiber with and without S. Typhimurium yielded a lower Firmicutes/Bacteroides ratio compared to other treatment groups, which is associated with poor gut health, and overall had greater changes to the cecal microbial community composition. However, changes in the total metabolome were primarily driven by the presence of S. Typhimurium. Additionally, the co-exposure to PE Fiber and S . Typhimurium caused greater cecal microbial community and metabolome changes than either exposure alone. Our results indicate that polymer shape is an important factor in effects resulting from exposure. It also demonstrates that microplastic-pathogen interactions cause metabolic alterations to the chicken cecal microbiome in an in vitro chicken cecal model.<br><br>IMPORTANCE: Researching the exposome, a summation of exposure of one's lifespan, will aid in determining the environmental factors that contribute to disease states. There is an emerging concern that microplastic-pathogen interactions in the gastrointestinal tract of broiler chickens may lead to an increase in Salmonella infection across flocks and eventually increased incidence of human salmonellosis cases. In this research article, we elucidated the effects of co-exposure to polyethylene microplastics and Salmonella enterica serovar Typhimurium on the ceca microbial community. Salmonella presence caused strong shifts in the cecal metabolome but not the microbiome. The inverse was true for polyethylene fiber. Polyethylene powder had almost no effect. The co-exposure had worse effects than either alone. This demonstrates that exposure effects to the gut microbial community are contaminant specific. When combined, the interactions between exposures exacerbate changes to the gut environment. The results herein support current Salmonella mitigation efforts and understanding microplastics-pathogen interactions.}, }
@article {pmid38045052, year = {2023}, author = {Zhang, K and Chen, L and Yang, J and Liu, J and Li, J and Liu, Y and Li, X and Chen, L and Hsu, C and Zeng, J and Xie, X and Wang, Q}, title = {Gut microbiota-derived short-chain fatty acids ameliorate methamphetamine-induced depression- and anxiety-like behaviors in a Sigmar-1 receptor-dependent manner.}, journal = {Acta pharmaceutica Sinica. B}, volume = {13}, number = {12}, pages = {4801-4822}, pmid = {38045052}, issn = {2211-3835}, abstract = {Methamphetamine (Meth) abuse can cause serious mental disorders, including anxiety and depression. The gut microbiota is a crucial contributor to maintaining host mental health. Here, we aim to investigate if microbiota participate in Meth-induced mental disorders, and the potential mechanisms involved. Here, 15 mg/kg Meth resulted in anxiety- and depression-like behaviors of mice successfully and suppressed the Sigma-1 receptor (SIGMAR1)/BDNF/TRKB pathway in the hippocampus. Meanwhile, Meth impaired gut homeostasis by arousing the Toll-like receptor 4 (TLR4)-related colonic inflammation, disturbing the gut microbiome and reducing the microbiota-derived short-chain fatty acids (SCFAs). Moreover, fecal microbiota from Meth-administrated mice mediated the colonic inflammation and reproduced anxiety- and depression-like behaviors in recipients. Further, SCFAs supplementation optimized Meth-induced microbial dysbiosis, ameliorated colonic inflammation, and repressed anxiety- and depression-like behaviors. Finally, Sigmar1 knockout (Sigmar1[-/-]) repressed the BDNF/TRKB pathway and produced similar behavioral phenotypes with Meth exposure, and eliminated the anti-anxiety and -depression effects of SCFAs. The activation of SIGMAR1 with fluvoxamine attenuated Meth-induced anxiety- and depression-like behaviors. Our findings indicated that gut microbiota-derived SCFAs could optimize gut homeostasis, and ameliorate Meth-induced mental disorders in a SIGMAR1-dependent manner. This study confirms the crucial role of microbiota in Meth-related mental disorders and provides a potential preemptive therapy.}, }
@article {pmid38045012, year = {2023}, author = {Medeot, DB and Nilson, A and Miazzo, RD and Grosso, V and Ferrari, W and Jofré, E and Soltermann, A and Peralta, MF}, title = {Stevia as a natural additive on gut health and cecal microbiota in broilers.}, journal = {Veterinary and animal science}, volume = {22}, number = {}, pages = {100322}, pmid = {38045012}, issn = {2451-943X}, abstract = {Stevia mash (SM), leaves of Stevia rebaudiana Bertoni plant, is an additive used in poultry that enhances growth and health. Objective: to determine the effect of 1 % SM on productive parameters, gut health, and the cecal microbiome in broilers between the first 15 and 21 days old. One hundred sixty male, 1-day-old broilers (48.5 ± 2.5 g) were divided into Control (C) without SM and Treated (T) with 1 % SM on diet, during 15/21 days. Each subgroup had eight broilers/five repetitions/treatment. At day 15 or 21, all broilers were dissected, Fabricius Bursa and Gut removed and processed for histomorphometry, followed by Villi Height/Crypt Deep (VH/CD) ratio. Conversion Index (CI) was determined. The V3-V4 region of 16S rRNA gene was amplified from DNA obtained from pooled cecal contents and sequenced on Illumina Miseq PE 2 × 250 platform. Sequence processing and taxonomic assignments were performed using the SHAMAN pipeline. Both T groups have better VH/CD Ratios than C groups (p ≤ 0.05). In guts, increased plasmatic and goblet cells number and thicker mucus layer were found in T15 and T21. All groups received SM showed early immunological maturity in Fabricius Bursa. IC was similar between all treatments. Faecalibacterium, Ruminococcus torques group, and Bacteroides were the major genera modulated by SM addition. At 15 and 21 days old, SM exerts a impact on diversity and evenness of the cecal microbiome. Conclusion: SM (1 %) produced early immunologic maturity on Fabricius Bursa, increased intestinal functionality, and modified the microbiota, increasing beneficial microbial genera and microbial diversity.}, }
@article {pmid38044555, year = {2023}, author = {Wang, L and George, TS and Feng, G}, title = {Concepts and consequences of the hyphosphere core microbiome for arbuscular mycorrhizal fungal fitness and function.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.19396}, pmid = {38044555}, issn = {1469-8137}, support = {32272807//National Natural Science Foundation of China/ ; }, abstract = {Arbuscular mycorrhizal (AM) fungi-associated hyphosphere microbiomes can be considered as the second genome of the mycorrhizal phosphorus uptake pathway. Their composition can be thought of as a stably recurring component of a holobiont, defined by the hyphosphere core microbiome, which is thought to benefit AM fungal fitness. Here, we review evidence indicating the existence of the hyphosphere core microbiome, highlight its functions linked to those functions lacking in AM fungi, and further explore the mechanisms by which different core members ensure their stable coexistence. We conclude that deciphering and utilizing the hyphosphere core microbiome provides an entry point for understanding the complex interactions among plants, AM fungi, and bacteria.}, }
@article {pmid38044504, year = {2023}, author = {Meade, S and Liu Chen Kiow, J and Massaro, C and Kaur, G and Squirell, E and Bressler, B and Lunken, G}, title = {Gut microbiome-associated predictors as biomarkers of response to advanced therapies in inflammatory bowel disease: a systematic review.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2287073}, doi = {10.1080/19490976.2023.2287073}, pmid = {38044504}, issn = {1949-0984}, abstract = {Loss of response to therapy in inflammatory bowel disease (IBD) has led to a surge in research focusing on precision medicine. Three systematic reviews have been published investigating the associations between gut microbiota and disease activity or IBD therapy. We performed a systematic review to investigate the microbiome predictors of response to advanced therapy in IBD. Unlike previous studies, our review focused on predictors of response to therapy; so the included studies assessed microbiome predictors before the proposed time of response or remission. We also provide an update of the available data on mycobiomes and viromes. We highlight key themes in the literature that may serve as future biomarkers of treatment response: the abundance of fecal SCFA-producing bacteria and opportunistic bacteria, metabolic pathways related to butyrate synthesis, and non-butyrate metabolomic predictors, including bile acids (BAs), amino acids, and lipids, as well as mycobiome predictors of response.}, }
@article {pmid38044445, year = {2023}, author = {Xiong, D and Zhang, L and Sun, ZJ}, title = {Targeting the epigenome to reinvigorate T cells for cancer immunotherapy.}, journal = {Military Medical Research}, volume = {10}, number = {1}, pages = {59}, pmid = {38044445}, issn = {2054-9369}, support = {82273202//National Natural Science Foundation of China/ ; 82072996//National Natural Science Foundation of China/ ; 82170941//National Natural Science Foundation of China/ ; 81974148//National Natural Science Foundation of China/ ; }, abstract = {Cancer immunotherapy using immune-checkpoint inhibitors (ICIs) has revolutionized the field of cancer treatment; however, ICI efficacy is constrained by progressive dysfunction of CD8[+] tumor-infiltrating lymphocytes (TILs), which is termed T cell exhaustion. This process is driven by diverse extrinsic factors across heterogeneous tumor immune microenvironment (TIME). Simultaneously, tumorigenesis entails robust reshaping of the epigenetic landscape, potentially instigating T cell exhaustion. In this review, we summarize the epigenetic mechanisms governing tumor microenvironmental cues leading to T cell exhaustion, and discuss therapeutic potential of targeting epigenetic regulators for immunotherapies. Finally, we outline conceptual and technical advances in developing potential treatment paradigms involving immunostimulatory agents and epigenetic therapies.}, }
@article {pmid38044401, year = {2023}, author = {Yan, Z and Wang, Z and Si, G and Chen, G and Feng, T and Liu, C and Chen, J}, title = {Bacteria-loaded biochar for the immobilization of cadmium in an alkaline-polluted soil.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {38044401}, issn = {1614-7499}, support = {202201BF070001-002, 202201AS070016//Natural Science Foundation of Yunnan Province/ ; }, abstract = {The combination of biochar and bacteria is a promising strategy for the remediation of Cd-polluted soils. However, the synergistic mechanisms of biochar and bacteria for Cd immobilization remain unclear. In this study, the experiments were conducted to evaluate the effects of the combination of biochar and Pseudomonas sp. AN-B15, on Cd immobilization, soil enzyme activity, and soil microbiome. The results showed that biochar could directly reduce the motility of Cd through adsorption and formation of CdCO3 precipitates, thereby protecting bacteria from Cd toxicity in the solution. In addition, bacterial growth further induces the formation of CdCO3 and CdS and enhances Cd adsorption by bacterial cells, resulting in a higher Cd removal rate. Thus, bacterial inoculation significantly enhances Cd removal in the presence of biochar in the solution. Moreover, soil incubation experiments showed that bacteria-loaded biochar significantly reduced soil exchangeable Cd in comparison with other treatments by impacting soil microbiome. In particular, bacteria-loaded biochar increased the relative abundance of Bacillus, Lysobacter, and Pontibacter, causing an increase in pH, urease, and arylsulfatase, thereby passivating soil exchangeable Cd and improving soil environmental quality in the natural alkaline Cd-contaminated soil. Overall, this study provides a systematic understanding of the synergistic mechanisms of biochar and bacteria for Cd immobilization in soil and new insights into the selection of functional strain for the efficient remediation of the contaminated environments by bacterial biochar composite.}, }
@article {pmid38043908, year = {2023}, author = {Kiran, NS and Yashaswini, C and Chatterjee, A}, title = {Noxious ramifications of cosmetic pollutants on gastrointestinal microbiome: A pathway to neurological disorders.}, journal = {Life sciences}, volume = {}, number = {}, pages = {122311}, doi = {10.1016/j.lfs.2023.122311}, pmid = {38043908}, issn = {1879-0631}, abstract = {On exposure to cosmetic pollutants, gastrointestinal dysbiosis, which is characterised by a disturbance in the gut microbiota, has come into focus as a possible contributor to the occurrence of neurotoxic consequences. It is normal practice to use personal care products that include parabens, phthalates, sulphates, triclosans/triclocarbans and micro/nano plastics. These substances have been found in a variety of bodily fluids and tissues, demonstrating their systemic dispersion. Being exposed to these cosmetic pollutants has been linked in recent research to neurotoxicity, including cognitive decline and neurodevelopmental problems. A vital part of sustaining gut health and general well-being is the gut flora. Increased intestinal permeability, persistent inflammation, and impaired metabolism may result from disruption of the gut microbial environment, which may in turn contribute to neurotoxicity. The link between gastrointestinal dysbiosis and the neurotoxic effects brought on by cosmetic pollutants may be explained by a number of processes, primarily the gut-brain axis. For the purpose of creating preventative and therapeutic measures, it is crucial to comprehend the intricate interactions involving cosmetic pollutants, gastrointestinal dysbiosis, and neurotoxicity. This review provides an in-depth understanding of the various hazardous cosmetic pollutants and its potential role in the occurrence of neurological disorders via gastrointestinal dysbiosis, providing insights into various described and hypothetical mechanisms regarding the complex toxic effects of these industrial pollutants.}, }
@article {pmid38043895, year = {2023}, author = {Li, Y and Li, R and Hou, J and Sun, X and Wang, Y and Li, L and Yang, F and Yao, Y and An, Y}, title = {Mobilome affect the dissemination of antibiotic resistance genes (ARGs) of clinical importance into the natural environment.}, journal = {Environmental research}, volume = {}, number = {}, pages = {117801}, doi = {10.1016/j.envres.2023.117801}, pmid = {38043895}, issn = {1096-0953}, abstract = {The prevalence of antibiotic resistance genes (ARGs) in the environment is a quintessential One Health issue that threats both human and ecosystem health; however, the source and transmission of ARGs, especially clinically important ARGs (CLIARGs), in the environment has not yet been well studied. In the present study, shotgun metagenomic approaches were used to characterize the microbiome, resistome, and mobilome composition in human feces and six different environment sample types in South China. Overall, the resistome harbored 157 CLIARGs, with specific ARG hotspots (e.g., human feces, wastewater treatment plants, livestock manure and wastewater) excreting significantly higher abundance of CLIARGs compared with the natural environment. A redundancy analysis (RDA) analysis was performed and revealed that the bacterial community compositions and mobile genetic elements (MGEs) explained 55.08% and 34.68% of the variations in ARG abundance, respectively, indicating that both bacterial community and MGEs are key contributors to the maintenance and dissemination of CLIARGs in environment. The network analysis revealed non-random co-occurrence patterns between 200 bacterial genera and 147 CLIARGs, as well as between 135 mobile genetic elements (MGEs) and 123 CLIARGs. In addition to numerous co-shared CLIARGs among different sample types, the source tracking program based on the FEAST probabilistic model was used to estimate the relative contributions of the CLIARGs from potential sources to the natural environment. The source tracking analysis results delineated that mobilome, more than microbiome, contributed CLIARG transmission from those ARG hotspots into natural environment, and the MGEs in WWTPs seems to played the most significant role in the spread of CLIARGs to the natural environment (average contribution 32.9%-46.4%). Overall, this study demonstrated the distribution and dissemination of CLIARGs in the environment, and aimed to better inform strategies to control the spread of CLIARGs into the natural environment.}, }
@article {pmid38043771, year = {2023}, author = {Higo, M and Kang, DJ and Isobe, K}, title = {Root-associated microbial community and diversity in napiergrass across radiocesium-contaminated lands after the Fukushima-Daiichi nuclear disaster in Japan.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {123051}, doi = {10.1016/j.envpol.2023.123051}, pmid = {38043771}, issn = {1873-6424}, abstract = {The microbiome derived from soil associated with plant roots help in plant growth and stress resistance. It exhibits potential benefits for soil remediation and restoration of radioactive-cesium ([137]Cs)-contaminated soils. However, there is still limited information about the community and diversity of root-associated microbiome in [137]Cs-contaminated soil after the Fukushima-Daiichi Nuclear Power Plant (FDNPP) disaster. To address this, a comparative analysis of communities and diversity of root-associated microbiomes was conducted in two field types after the FDNPP disaster. In 2013, we investigated the community and diversity of indigenous root-associated microbiome of napiergrass (Pennisetum purpureum) grown in both grassland and paddy fields of [137]Cs-contaminated land-use type within a 30-km radius around the FDNPP. Results showed that the root-associated bacterial communities in napiergrass belonged to 32 phyla, 75 classes, 174 orders, 284 families, and 521 genera, whereas the root-associated fungal communities belonged to 5 phyla, 11 classes, 31 orders, 59 families, and 64 genera. The most frequently observed phylum in both grassland and paddy field was Proteobacteria (47.4% and 55.9%, respectively), followed by Actinobacteriota (23.8% and 27.9%, respectively) and Bacteroidota (10.1% and 11.3%, respectively). The dominant fungal phylum observed in both grassland and paddy field was Basidiomycota (75.9% and 94.2%, respectively), followed by Ascomycota (24.0% and 5.8%, respectively). Land-use type significantly affected the bacterial and fungal communities that colonize the roots of napiergrass. Several [137]Cs-tolerant bacterial and fungal taxa were also identified, which may be potentially applied for the phytoremediation of [137]Cs-contaminated areas around FDNPP. These findings contribute to a better understanding of the distribution of microbial communities in [137]Cs-contaminated lands and their long-term ecosystem benefits for phytoremediation efforts.}, }
@article {pmid38043766, year = {2023}, author = {Sabatino, R and Sbaffi, T and Corno, G and Cabello-Yeves, PJ and Di Cesare, A}, title = {The diversity of the antimicrobial resistome of lake Tanganyika increases with the water depth.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {342}, number = {}, pages = {123065}, doi = {10.1016/j.envpol.2023.123065}, pmid = {38043766}, issn = {1873-6424}, abstract = {The presence of antimicrobial resistance genes (ARGs) in the microbiome of freshwater communities is a consequence of thousands of years of evolution but also of the pressure exerted by anthropogenic activities, with potential negative impact on environmental and human health. In this study, we investigated the distribution of ARGs in Lake Tanganyika (LT)'s water column to define the resistome of this ancient lake. Additionally, we compared the resistome of LT with that of Lake Baikal (LB), the oldest known lake with different environmental characteristics and a lower anthropogenic pollution than LT. We found that richness and abundance of several antimicrobial resistance classes were higher in the deep water layers in both lakes. LT Kigoma region, known for its higher anthropogenic pollution, showed a greater richness and number of ARG positive MAGs compared to Mahale. Our results provide a comprehensive understanding of the antimicrobial resistome of LT and underscore its importance as reservoir of antimicrobial resistance. In particular, the deepest water layers of LT are the main repository of diverse ARGs, mirroring what was observed in LB and in other aquatic ecosystems. These findings suggest that the deep waters might play a crucial role in the preservation of ARGs in aquatic ecosystems.}, }
@article {pmid38043414, year = {2023}, author = {Chen, X and Zhu, D and Zhang, F and Li, O and Yang, F and Bao, Z}, title = {Exposure to triphenyltin impairs gut integrity, disturbs gut microbiota, and alters fecal metabolites.}, journal = {Ecotoxicology and environmental safety}, volume = {269}, number = {}, pages = {115753}, doi = {10.1016/j.ecoenv.2023.115753}, pmid = {38043414}, issn = {1090-2414}, abstract = {Triphenyltin is an environmental contaminant widely used in antifouling paints and can cause toxicity in various organs in living organisms. However, its effects on intestinal function and the microbiome of the gut remain unknown. The objective of this study was to explore the intestinal toxicity of triphenyltin in mice by orally administering 0, 1.875, 3.75, and 7.5 mg/Kg to adult male mice for 8 weeks. Results showed that triphenyltin caused ileum tissue damage, induced oxidative stress, upregulated inflammation-related gene expression and increased serum tumor-necrosis factor α (TNF-α) levels in mice. Triphenyltin impaired ileum barrier function by downregulating Muc2, ZO-1, Occludin and their protein levels at 3.75 and 7.5 mg/Kg. TPT exposure led to partial inflammation and decreased mucin mRNA expression in the colon. Triphenyltin altered intestinal micro-ecological balance and fecal metabolome in mice. In conclusion, triphenyltin alters the mouse gut microbiota and fecal metabolome.}, }
@article {pmid38043315, year = {2023}, author = {Zhou, SY and Yang, K and Neilson, R and Li, H and Li, HZ and Zhou, YY and Liu, J and Su, JQ and Huang, FY}, title = {Long-term seawall barriers lead to the formation of an urban coastal lagoon with increased antibiotic resistome.}, journal = {Journal of environmental management}, volume = {351}, number = {}, pages = {119721}, doi = {10.1016/j.jenvman.2023.119721}, pmid = {38043315}, issn = {1095-8630}, abstract = {Urbanization has increased the spread of antibiotic resistance genes (ARGs) impacting urban aquatic ecosystems and threatening human health. However, an overview of the antibiotic resistome in artificial coastal lagoons formed by coastal seawall construction is unclear. This study investigated the resistome of sediment in a coastal lagoon, established for over 60 years and found that the composition of the resistome in the lagoon sediments associated with the seawall significantly differed from that of marine sediment external to the seawall. Moreover, the diversity, number, relative abundance, and absolute abundance of the antibiotic resistome in the lagoon sediments were significantly higher compared to marine sediment. Network analyses revealed that more co-occurrences were found in lagoon sediment between bacterial communities, ARGs and mobile genetic elements (MGEs) than in marine sediments, suggesting that bacteria in lagoon sediments may be associated with multiple antibiotic resistances. Random forest and structural equation models showed that an increase in the absolute abundance of MGEs had a concomitant effect on the absolute abundance and diversity of ARGs, whereas increasing salinity decreased the absolute abundance of ARGs. This study provides a basis to assess the risk of resistome diffusion and persistence in an artificial coastal lagoon.}, }
@article {pmid38042865, year = {2023}, author = {Daybog, I and Kolodny, O}, title = {A computational framework for resolving the microbiome diversity conundrum.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7977}, pmid = {38042865}, issn = {2041-1723}, support = {1826/20//Israel Science Foundation (ISF)/ ; 9341//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; }, mesh = {Humans ; *Bacteria/genetics ; *Microbiota/genetics ; Phenotype ; }, abstract = {Recent empirical studies offer conflicting findings regarding the relation between host fitness and the composition of its microbiome, a conflict which we term 'the microbial β- diversity conundrum'. The microbiome is crucial for host wellbeing and survival. Surprisingly, different healthy individuals' microbiome compositions, even in the same population, often differ dramatically, contrary to the notion that a vital trait should be highly conserved. Moreover, gnotobiotic individuals exhibit highly deleterious phenotypes, supporting the view that the microbiome is paramount to host fitness. However, the introduction of almost arbitrarily selected microbiota into the system often achieves a significant rescue effect of the deleterious phenotypes. This is true even for microbiota from soil or phylogenetically distant host species, highlighting an apparent paradox. We suggest several solutions to the paradox using a computational framework, simulating the population dynamics of hosts and their microbiomes over multiple generations. The answers invoke factors such as host population size, the specific mode of microbial contribution to host fitness, and typical microbiome richness, offering solutions to the conundrum by highlighting scenarios where even when a host's fitness is determined in full by its microbiome composition, this composition has little effect on the natural selection dynamics of the population.}, }
@article {pmid38042820, year = {2023}, author = {Swarte, JC and Knobbe, TJ and Björk, JR and Gacesa, R and Nieuwenhuis, LM and Zhang, S and Vila, AV and Kremer, D and Douwes, RM and Post, A and Quint, EE and Pol, RA and Jansen, BH and ,  and de Borst, MH and de Meijer, VE and Blokzijl, H and Berger, SP and Festen, EAM and Zhernakova, A and Fu, J and Harmsen, HJM and Bakker, SJL and Weersma, RK}, title = {Health-related quality of life is linked to the gut microbiome in kidney transplant recipients.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7968}, pmid = {38042820}, issn = {2041-1723}, mesh = {Humans ; Quality of Life ; *Gastrointestinal Microbiome/genetics ; *Kidney Transplantation/adverse effects ; Feces/microbiology ; Dysbiosis/microbiology ; }, abstract = {Kidney transplant recipients (KTR) have impaired health-related quality of life (HRQoL) and suffer from intestinal dysbiosis. Increasing evidence shows that gut health and HRQoL are tightly related in the general population. Here, we investigate the association between the gut microbiome and HRQoL in KTR, using metagenomic sequencing data from fecal samples collected from 507 KTR. Multiple bacterial species are associated with lower HRQoL, many of which have previously been associated with adverse health conditions. Gut microbiome distance to the general population is highest among KTR with an impaired physical HRQoL (R = -0.20, P = 2.3 × 10[-65]) and mental HRQoL (R = -0.14, P = 1.3 × 10[-3]). Physical and mental HRQoL explain a significant part of variance in the gut microbiome (R[2] = 0.58%, FDR = 5.43 × 10[-4] and R[2] = 0.37%, FDR = 1.38 × 10[-3], respectively). Additionally, multiple metabolic and neuroactive pathways (gut brain modules) are associated with lower HRQoL. While the observational design of our study does not allow us to analyze causality, we provide a comprehensive overview of the associations between the gut microbiome and HRQoL while controlling for confounders.}, }
@article {pmid38042512, year = {2023}, author = {Zhou, X and Ruan, W and Wang, T and Liu, H and Du, L and Huang, J}, title = {Exploring the Impact of Gut Microbiota on Abdominal Aortic Aneurysm Risk through a Bidirectional Mendelian Randomization Analysis.}, journal = {Journal of vascular surgery}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jvs.2023.11.041}, pmid = {38042512}, issn = {1097-6809}, abstract = {OBJECTIVE: The abdominal aortic aneurysm (AAA) is associated with alterations in the composition of the gut microbiota; however, the precise causal relationship remains unclear. Elucidating this complex interplay could provide new insights into the pathogenesis of AAA.<br><br>METHODS: A bidirectional two-sample Mendelian randomization analysis was conducted utilizing genome-wide association study summary data on the gut microbiota (n=18,340) and AAA (n=353,087). A total of 196 gut microbial taxa across taxonomic levels were examined for their potential causal effects on AAA risk. Conversely, the effect of AAA on these microbial taxa was also analyzed.<br><br>RESULTS: Nine microbial taxa were identified as having a causal influence on AAA risk. Specifically, increased risk were associated with genus Bilophila (OR = 1.359, P = 0.0119), genus Catenibacterium (OR = 1.348, P = 0.0058), genus Family XIII AD3011 group (OR = 1.507, P = 0.004), genus Oxalobacter (OR = 1.157, P = 0.0449), and genus Prevotella 7 (OR = 1.194, P = 0.0306), whereas decreased risks were linked to class Lentisphaeria (OR = 0.829, P = 0.0361), order Victivallales (OR = 0.829, P = 0.0361), family Victivallaceae (OR = 0.814, P = 0.0057), and genus Anaerotruncus (OR = 0.773, P = 0.0497). Furthermore, AAA was found to influence the abundance of 14 microbial taxa across various taxonomic levels. Notably, bidirectional associations were observed with the class Lentisphaeria and the order Victivallales.<br><br>CONCLUSIONS: This study provides novel evidence for a reciprocal causal relationship between gut microbiota and AAA risk, thereby offering new insights into the pathogenesis of AAA. These findings also suggest promising avenues for microbiome-based therapeutic interventions.}, }
@article {pmid38042412, year = {2023}, author = {Mikulic, N and Uyoga, MA and Stoffel, NU and Derrien, M and Nyilima, S and Kostopoulos, I and Roeselers, G and Chenoll, E and Mwasi, E and Pironaci, G and Karanja, S and Bourdet-Sicard, R and Zimmermann, MB}, title = {Prebiotics increase iron absorption and reduce the adverse effects of iron on the gut microbiome and inflammation: a randomized controlled trial using iron stable isotopes in Kenyan infants.}, journal = {The American journal of clinical nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajcnut.2023.11.018}, pmid = {38042412}, issn = {1938-3207}, abstract = {BACKGROUND: Iron fortificants tend to be poorly absorbed and may adversely affect the gut, especially in African children.<br><br>OBJECTIVE: We assessed the effects of prebiotic galacto-oligosaccharides/fructo-oligosaccharides (GOS/FOS) on iron absorption and gut health when added to iron-fortified infant cereal.<br><br>METHODS: We randomized Kenyan infants (n=191) to receive daily for 3 weeks a cereal containing iron and either 7.5g GOS/FOS (7.5g+iron group), 3g (3g+iron group) GOS/FOS, or no prebiotics (iron group). A subset of infants in the two prebiotic+iron groups (n=66) consumed 4 stable iron isotope labelled test meals without and with prebiotics, both before and after the intervention. Primary outcome was fractional iron absorption (FIA) from the cereal with or without prebiotics regardless of dose, before and after 3 weeks of consumption. Secondary outcomes included: fecal gut microbiota, iron and inflammation status, and effects of prebiotic dose. We registered the study at Clinicaltrials.gov(NCT03894358).<br><br>RESULTS: Median(25th-75th percentiles) FIAs from meals before intervention were: 16.3%[8.0-27.6] without prebiotics versus 20.5%[10.4-33.4] with prebiotics (Cohen's d=0.53; P<0.001). FIA from the meal consumed without prebiotics after intervention was 22.9%[8.5-32.4], 41% higher than from the meal without prebiotics before intervention (Cohen's d=0.36; P=0.002). FIA from the meal consumed with prebiotics after intervention was 26.0%[12.2-36.1], 60% higher than from the meal without prebiotics before intervention (Cohen's d=0.45; P=0.007). After 3 weeks, compared to the iron group: (i) Lactobacillus abundances were higher in both prebiotic+iron groups (P<0.05); (ii) Enterobacteriaceae abundances (P=0.022) and the sum of pathogens (P<0.001) were lower in the 7.5g+iron group; (iii) the abundance of bacterial toxin-encoding genes was lower in the 3g+iron group (FDR<0.05); (iv) fecal pH (P<0.001) and calprotectin (P=0.033) were lower in the 7.5g+iron group.<br><br>CONCLUSIONS: Adding prebiotics to iron-fortified infant cereal increases iron absorption and reduces the adverse effects of iron on the gut microbiome and inflammation in Kenyan infants.}, }
@article {pmid38042352, year = {2023}, author = {Stinson, LF and George, A and Gridneva, Z and Jin, X and Lai, CT and Geddes, DT}, title = {Effects of different thawing and warming processes on human milk composition.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tjnut.2023.11.027}, pmid = {38042352}, issn = {1541-6100}, abstract = {The composition of human milk is influenced by storage and processing practices. The effects of thawing and warming practices on human milk composition remain poorly studied despite their prevalence in home, research, and donor milk bank settings. This review comprehensively examines the impact of different thawing and warming methods on nutritional and bioactive human milk components. While some components such as carbohydrates and minerals remain stable under most typical thawing and warming conditions, others, such as fat, immune proteins, bacterial and human cells, and peptide amine hormones, are sensitive to warming. This review has identified that the data on the effects of milk thawing and warming is limited and often contradictory. Given that numerous important components of milk are diminished during cold storage, it is important that thawing and warming practices do not lead to further loss of or alterations to beneficial milk components. Further work in this field will facilitate greater standardisation of thawing methods among researchers and underpin recommendations for thawing and warming of expressed milk for parents.}, }
@article {pmid38042328, year = {2023}, author = {Kimmel, MC and Verosky, B and Chen, HJ and Davis, O and Gur, TL}, title = {The Maternal Microbiome as a Map to Understanding the Impact of Prenatal Stress on Offspring Psychiatric Health.}, journal = {Biological psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.biopsych.2023.11.014}, pmid = {38042328}, issn = {1873-2402}, abstract = {Stress and psychiatric disorders have been independently associated with disruption of the maternal and offspring microbiome, and with increased risk of the offspring developing psychiatric disorders, both in clinical studies and in preclinical studies. However, the role of the microbiome in mediating the effect of prenatal stress on offspring behavior is unclear. While preclinical studies have identified several key mechanisms, clinical studies focusing on mechanisms are limited. In this review, we discuss three specific mechanisms by which the microbiome could mediate the effects of prenatal stress: 1) altered production of SCFAs; 2) disruptions in Th17 cell differentiation, leading to maternal and fetal immune activation; and 3) perturbation of intestinal and microbial tryptophan metabolism and serotonergic signaling. Finally, we review the existing clinical literature focusing on these mechanisms and highlight the need for additional mechanistic clinical research to better understand the role of the microbiome in the context of prenatal stress.}, }
@article {pmid38042287, year = {2023}, author = {Tan, H and Shi, Y and Yue, T and Zheng, D and Luo, S and Weng, J and Zheng, X}, title = {Machine learning approach reveals microbiome, metabolome, and lipidome profiles in type 1 diabetes.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2023.11.025}, pmid = {38042287}, issn = {2090-1224}, abstract = {INTRODUCTION: Type 1 diabetes (T1D) is a complex disorder influenced by genetic and environmental factors. The gut microbiome, the serum metabolome, and the serum lipidome have been identified as key environmental factors contributing to the pathophysiological mechanisms of T1D.<br><br>OBJECTIVES: We aimed to explore the gut microbiota, serum metabolite, and serum lipid signatures in T1D patients by machine learning.<br><br>METHODS: We evaluated 137 individuals in a cross-sectional cohort involving 38 T1D patients, 38 healthy controls, and 61 T1D patients for validation. We characterized gut microbiome, serum metabolite, and serum lipid profiles with machine learning approaches (logistic regression, support vector machine, Gaussian naive Bayes, and random forest).<br><br>RESULTS: The machine learning approaches using the microbiota composition did not accurately diagnose T1D (model accuracy&#xa0;=&#xa0;0.7555), while the accuracy of the model using the metabolite composition was 0.9333. Based on the metabolite composition, 3-hydroxybutyric acid and 9-oxo-ode (area under curve&#xa0;=&#xa0;0.70 and 0.67, respectively, both increased in T1D) were meaningful overlap metabolites screened by multiple bioinformatics methods. We confirmed the biological relevance of the microbiome, metabolome, and lipidome features in the validation group.<br><br>CONCLUSION: By using machine learning algorithms and multi-omics, we demonstrated that T1D patients are associated with altered microbiota, metabolite, and lipidomic signatures or functions.}, }
@article {pmid38042069, year = {2023}, author = {Zhao, Y and Yu, S and Tan, J and Wang, Y and Li, L and Zhao, H and Liu, M and Jiang, L}, title = {Bioconversion of citrus waste by long-term DMSO-cryopreserved rumen fluid to volatile fatty acids and biogas is feasible: A microbiome perspective.}, journal = {Journal of environmental management}, volume = {351}, number = {}, pages = {119693}, doi = {10.1016/j.jenvman.2023.119693}, pmid = {38042069}, issn = {1095-8630}, abstract = {Preserving rumen fluid as the inoculum for anaerobic digestion of food waste is necessary when access to animal donors or slaughterhouses is limited. This study aims to compare two preservation methods relative to fresh ruminal inoculum: (1) cryoprotected with 5% dimethyl sulfoxide (DMSO) and stored at -20 °C and (2) frozen at -20 °C, both for 6 months. The fermentation activity of different inoculum was evaluated by rumen-based in vitro anaerobic fermentation tests (volatile fatty acids, biomass digestibility, and gas production). Citrus pomace was used as the substrate during a 96-h fermentation. The maximum volatile fatty acids, methane production, and citrus pomace digestibility from fresh rumen fluid were not significantly different from rumen fluid preserved with DMSO. Metagenome analysis revealed a significant difference in the rumen microbial composition and functions between fresh rumen fluid and frozen inoculum without DMSO. Storage of rumen fluid using -20 °C with DMSO demonstrated the less difference compared with fresh rumen fluid in microbial alpha diversity and taxa composition. The hierarchical clustering tree of CAZymes showed that DMSO cryoprotected fluid was clustered much closer to the fresh rumen fluid, showing more similarity in CAZyme profiles than frozen rumen fluid. The abundance of functional genes associated with carbohydrate metabolism and methane metabolism did not differ between fresh rumen fluid and the DMSO-20 °C, whereas the abundance of key functional genes significantly decreased in frozen rumen fluid. These findings suggest that using rumen liquid preserved using DMSO at -20 °C for 180 days is a feasible alternative to fresh rumen fluid. This would reduce the need for laboratories to maintain animal donors and/or reduce the frequency of collecting rumen fluid from slaughterhouses.}, }
@article {pmid38042039, year = {2023}, author = {Yan, H and Xu, G and Bei, L and Jiang, S and Zhang, R}, title = {Duck hepatitis A virus type 1 infection induces hepatic metabolite and gut microbiota changes in ducklings.}, journal = {Poultry science}, volume = {103}, number = {2}, pages = {103265}, doi = {10.1016/j.psj.2023.103265}, pmid = {38042039}, issn = {1525-3171}, abstract = {Duck hepatitis A virus type 1 (DHAV-1) can cause severe liver damage in infected ducklings and is a fatal and contagious pathogen that endangers the Chinese duck industry. The objective of this study was to explore the correlation mechanism of liver metabolism-gut microbiota in DHAV-1 infection. Briefly, liquid chromatography-mass spectrometry and 16S rDNA sequencing combined with multivariate statistical analysis were used to evaluate the effects of DHAV-1 infection on liver metabolism, gut microbiota regulation, and other potential mechanisms in ducklings. In DHAV-1-infected ducklings at 72 h postinfection, changes were found in metabolites associated with key metabolic pathways such as lipid metabolism, sugar metabolism, and nucleotide metabolism, which participated in signaling networks and ultimately affecting the function of the liver. The abundance and composition of gut microbiota were also changed, and gut microbiota is significantly involved in lipid metabolism in the liver. The evident correlation between gut microbiota and liver metabolites indicates that DHAV-host gut microbiome interactions play important roles in the development of duck viral hepatitis (DVH).}, }
@article {pmid38041547, year = {2023}, author = {Li, Y and Rao, G and Zhu, G and Cheng, C and Yuan, L and Li, C and Gao, J and Tang, J and Wang, Z and Li, W}, title = {Dysbiosis of lower respiratory tract microbiome are associated with proinflammatory states in non-small cell lung cancer patients.}, journal = {Thoracic cancer}, volume = {}, number = {}, pages = {}, doi = {10.1111/1759-7714.15166}, pmid = {38041547}, issn = {1759-7714}, abstract = {BACKGROUND: The lung has a sophisticated microbiome, and respiratory illnesses are greatly influenced by the lung microbiota. Despite the fact that numerous studies have shown that lung cancer patients have a dysbiosis as compared to healthy people, more research is needed to explore the association between the microbiota dysbiosis and immune profile within the tumor microenvironment (TME).<br><br>METHODS: In this study, we performed metagenomic sequencing of tumor and normal tissues from 61 non-small cell lung cancer (NSCLC) patients and six patients with other lung diseases. In order to characterize the impact of the microbes in TME, the cytokine concentrations of 24 lung tumor and normal tissues were detected using a multiple cytokine panel.<br><br>RESULTS: Our results showed that tumors had lower microbiota diversity than the paired normal tissues, and the microbiota of NSCLC was enriched in Proteobacteria, Firmicutes, and Actinobacteria. In addition, proinflammatory cytokines such as IL-8, MIF, TNF- &#x3b1;, and so on, were significantly upregulated in tumor tissues.<br><br>CONCLUSION: We discovered a subset of bacteria linked to host inflammatory signaling pathways and, more precisely, to particular immune cells. We determined that lower airway microbiome dysbiosis may be linked to the disruption of the equilibrium of the immune system causing lung inflammation. The spread of lung cancer may be linked to specific bacteria.}, }
@article {pmid38041542, year = {2023}, author = {Sampson, T}, title = {Microbial amyloids in neurodegenerative amyloid diseases.}, journal = {The FEBS journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/febs.17023}, pmid = {38041542}, issn = {1742-4658}, abstract = {Human-disease associated amyloidogenic proteins are not unique in their ability to form amyloid fibrillar structures. Numerous microbes produce amyloidogenic proteins that have distinct functions for their physiology in their amyloid form, rather than solely detrimental. Emerging data indicate associations between various microbial organisms, including those which produce functional amyloids, with neurodegenerative diseases. Here, we review some of the evidence suggesting that microbial amyloids impact amyloid disease in host organisms. Experimental data are building a foundation for continued lines of enquiry, and suggest that that direct or indirect interactions between microbial and host amyloids may be a contributor to amyloid pathologies. Inhibiting microbial amyloids or their interactions with the host, may therefore represent a tangible target to limit various amyloid pathologies.}, }
@article {pmid38041519, year = {2023}, author = {Vestergaard, MV and Allin, KH and Eriksen, C and Zakerska-Banaszak, O and Arasaradnam, RP and Alam, MT and Kristiansen, K and Brix, S and Jess, T}, title = {Gut microbiota signatures in inflammatory bowel disease.}, journal = {United European gastroenterology journal}, volume = {}, number = {}, pages = {}, doi = {10.1002/ueg2.12485}, pmid = {38041519}, issn = {2050-6414}, support = {DNRF148//Danmarks Grundforskningsfond/ ; }, abstract = {BACKGROUND: Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), affect millions of people worldwide with increasing incidence.<br><br>OBJECTIVES: Several studies have shown a link between gut microbiota composition and IBD, but results are often limited by small sample sizes. We aimed to re-analyze publicly available fecal microbiota data from IBD patients.<br><br>METHODS: We extracted original fecal 16S rRNA amplicon sequencing data from 45 cohorts of IBD patients and healthy individuals using the BioProject database at the National Center for Biotechnology Information. Unlike previous meta-analyses, we merged all study cohorts into a single dataset, including sex, age, geography, and disease information, based on which microbiota signatures were analyzed, while accounting for varying technical platforms.<br><br>RESULTS: Among 2518 individuals in the combined dataset, we discovered a hitherto unseen number of genera associated with IBD. A total of 77 genera associated with CD, of which 38 were novel associations, and a total of 64 genera associated with UC, of which 28 represented novel associations. Signatures were robust across different technical platforms and geographic locations. Reduced alpha diversity in IBD compared to healthy individuals, in CD compared to UC, and altered microbiota composition (beta diversity) in UC and especially in CD as compared to healthy individuals were found.<br><br>CONCLUSIONS: Combining original microbiota data from 45 cohorts, we identified a hitherto unseen large number of genera associated with IBD. Identification of microbiota features robustly associated with CD and UC may pave the way for the identification of new treatment targets.}, }
@article {pmid38041504, year = {2023}, author = {Fujimoto, A and Fujii, K and Suido, H and Fukuike, H and Miyake, N and Suzuki, H and Eguchi, T and Tobata, H}, title = {Changes in oral microflora following 0.3% cetylpyridinium chloride-containing mouth spray intervention in adult volunteers after professional oral care: Randomized clinical study.}, journal = {Clinical and experimental dental research}, volume = {}, number = {}, pages = {}, doi = {10.1002/cre2.810}, pmid = {38041504}, issn = {2057-4347}, support = {//Sunstar Inc./ ; }, abstract = {OBJECTIVES: This study explored the changes in bacterial flora composition and total bacterial count in the saliva and tongue coating, along with the change in the tongue coating index (TCI) following an intervention with 0.3% cetylpyridinium chloride (CPC) mouth spray after professional oral care.<br><br>MATERIALS AND METHODS: Fifty-two adult volunteers aged 30-60 years were equally divided into CPC spray (n&#x2009;=&#x2009;26) and control (n&#x2009;=&#x2009;26) groups. All subjects underwent scaling and polishing. The CPC spray group was administered four puffs of CPC spray to the tongue dorsum four times a day for 3 weeks. The control group performed only routine daily oral care (brushing) and did not use any other spray. Bacteriological evaluation of saliva and tongue coating was performed using 16S ribosomal RNA&#xa0;gene sequencing and quantitative polymerase chain reaction. The tongue coating was evaluated to calculate the TCI. A per-protocol analysis was conducted for 44 subjects (CPC spray group, n&#x2009;=&#x2009;23; control group, n&#x2009;=&#x2009;21).<br><br>RESULTS: At 1 and 3 weeks after CPC spray use, the flora of the saliva and tongue coating changed; the genus Haemophilus was dominant in the CPC spray group, whereas the genus Saccharibacteria was dominant in the control group. The sampling time differed among individual participants, which may have affected the bacterial counts. There was no significant intragroup change in TCI in either group.<br><br>CONCLUSIONS: CPC spray affected the bacterial flora in the saliva and tongue coating, particularly with respect to an increase in the abundance of Haemophilus. However, CPC spray did not change the TCI. These results suggest that it may be optimal to combine CPC spray with a physical cleaning method such as using a tongue brush or scraper.&#xa0;Clinical Trial Registration:&#xa0;University Hospital Medical Information Network UMIN000041140.}, }
@article {pmid38041152, year = {2023}, author = {McGurrin, A and Maguire, J and Tiwari, BK and Garcia-Vaquero, M}, title = {Anti-methanogenic potential of seaweeds and seaweed-derived compounds in ruminant feed: current perspectives, risks and future prospects.}, journal = {Journal of animal science and biotechnology}, volume = {14}, number = {1}, pages = {145}, pmid = {38041152}, issn = {1674-9782}, support = {EPSPG/2021/154//Irish Research Council/ ; Project No. 817992//BlueBio ERA-NET COFUND/ ; }, abstract = {With methane emissions from ruminant agriculture contributing 17% of total methane emissions worldwide, there is increasing urgency to develop strategies to reduce greenhouse gas emissions in this sector. One of the proposed strategies is ruminant feed intervention studies focused on the inclusion of anti-methanogenic compounds which are those capable of interacting with the rumen microbiome, reducing the capacity of ruminal microorganisms to produce methane. Recently, seaweeds have been investigated for their ability to reduce methane in ruminants in vitro and in vivo, with the greatest methane abatement reported when using the red seaweed Asparagopsis taxiformis (attributed to the bromoform content of this species). From the literature analysis in this study, levels of up to 99% reduction in ruminant methane emissions have been reported from inclusion of this seaweed in animal feed, although further in vivo and microbiome studies are required to confirm these results as other reports showed no effect on methane emission resulting from the inclusion of seaweed to basal feed. This review explores the current state of research aiming to integrate seaweeds as anti-methanogenic feed additives, as well as examining the specific bioactive compounds within seaweeds that are likely to be related to these effects. The effects of the inclusion of seaweeds on the ruminal microbiome are also reviewed, as well as the future challenges when considering the large-scale inclusion of seaweeds into ruminant diets as anti-methanogenic agents.}, }
@article {pmid38041127, year = {2023}, author = {Diaz, GR and Gaire, TN and Ferm, P and Case, L and Caixeta, LS and Goldsmith, TJ and Armstrong, J and Noyes, NR}, title = {Effect of castration timing and weaning strategy on the taxonomic and functional profile of ruminal bacteria and archaea of beef calves.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {61}, pmid = {38041127}, issn = {2524-4671}, support = {Grantee No. GNT-20212290//Fulbright Scholarship/ ; Contract No. 085-2020-FONDECYT//Consejo Nacional de Ciencia, Tecnologia e Innovacion Tecnologica from Peru/ ; MnDRIVE Graduate Student Professional Development award//MnDRIVE Global Food Ventures Program/ ; }, abstract = {BACKGROUND: Beef cattle experience several management challenges across their lifecycle. Castration and weaning, two major interventions in the early life of beef cattle, can have a substantial impact on animal performance. Despite the key role of the rumen microbiome on productive traits of beef cattle, the effect of castration timing and weaning strategy on this microbial community has not been formally described. We assessed the effect of four castration time windows (at birth, turnout, pre-weaning and weaning) and two weaning strategies (fence-line and truck transportation) on the rumen microbiome in a randomized controlled study with 32 male calves across 3 collection days (i.e., time points). Ruminal fluid samples were submitted to shotgun metagenomic sequencing and changes in the taxonomic (microbiota) and functional profile (metagenome) of the rumen microbiome were described.<br><br>RESULTS: Using a comprehensive yet stringent taxonomic classification approach, we identified 10,238 unique taxa classified under 40 bacterial and 7 archaeal phyla across all samples. Castration timing had a limited long-term impact on the rumen microbiota and was not associated with changes in alpha and beta diversity. The interaction of collection day and weaning strategy was associated with changes in the rumen microbiota, which experienced a significant decrease in alpha diversity and shifts in beta diversity within 48&#xa0;h post-weaning, especially in calves abruptly weaned by truck transportation. Calves weaned using a fence-line weaning strategy had lower relative abundance of Bacteroides, Lachnospira, Fibrobacter and Ruminococcus genera compared to calves weaned by truck transportation. Some genes involved in the hydrogenotrophic methanogenesis pathway (fwdB and fwdF) had higher relative abundance in fence-line-weaned calves post-weaning. The antimicrobial resistance gene tetW consistently represented more than 50% of the resistome across time, weaning and castration groups, without significant changes in relative abundance.<br><br>CONCLUSIONS: Within the context of this study, castration timing had limited long-term effects on the rumen microbiota, while weaning strategy had short-term effects on the rumen microbiota and methane-associated metagenome, but not on the rumen resistome.}, }
@article {pmid38041079, year = {2023}, author = {Hong, X and Qin, P and Gao, L and Huang, L and Shi, Y and Peng, D and Wang, B}, title = {Change of the vaginal microbiome with oral contraceptive therapy in women with polycystic ovary syndrome: a 6-month longitudinal cohort study.}, journal = {BMC medicine}, volume = {21}, number = {1}, pages = {478}, pmid = {38041079}, issn = {1741-7015}, support = {82204057//National Natural Science Foundation of China/ ; BK20220827//Basic Research Program of Jiangsu Province/ ; 2022M720713//Postdoctoral Research Foundation of China/ ; }, mesh = {Female ; Humans ; *Polycystic Ovary Syndrome/drug therapy ; Contraceptives, Oral ; Cohort Studies ; Longitudinal Studies ; RNA, Ribosomal, 16S/genetics ; Luteinizing Hormone ; Anti-Mullerian Hormone ; }, abstract = {BACKGROUND: The association between the vaginal microbiome and polycystic ovary syndrome (PCOS) is reported, but the longitudinal changes in the vaginal microbiome that accompany oral contraceptive therapy have not been described.<br><br>METHODS: This cohort study included 50 PCOS patients who wanted to make their menstrual periods more regular and accepted only oral contraceptive therapy and lifestyle coaching, then they were successfully followed up for 6&#xa0;months. Venous blood was collected, and follicle-stimulating hormone (FSH), luteinizing hormone (LH), total testosterone (T), anti-M&#xfc;llerian hormone (AMH), and estradiol (E2) were assayed at baseline and at months 3 and 6. Vaginal swabs were collected at baseline and at months&#xa0;3 and 6. 16S rRNA genes were sequenced to identify the microbiota structure. Latent class trajectory models were used to explore the trajectory of the changes in Lactobacillus abundance.<br><br>RESULTS: At 3&#xa0;months, all patients reported regular periods, and the improvement lasted until 6&#xa0;months. The body mass index and waist-to-hip ratio decreased with treatment (P&#x2009;<&#x2009;0.01), and the AMH and T levels showed downward trends. We did not find a statistically significant relationship between hormone levels at the previous time point and the vaginal microbiota at subsequent time points (P&#x2009;>&#x2009;0.05). The relative abundance of Lactobacillus increased with treatment, and trajectory analysis revealed five classes of Lactobacillus changes. Class 1, stable high level, accounted for 26%; class 2, decrease followed by increase, accounted for 18%; class 3, stable low level, accounted for 10%; class 4, increase, accounted for 20%; class 5, increase followed by decrease, accounted for 26%. Logistic models showed that compared to class 1, a higher baseline T level was associated with a reduced risk of class 2 change (odds ratio (OR)&#x2009;=&#x2009;0.03, 95% confidence interval (CI):0.01-0.52) and class 4 change (OR&#x2009;=&#x2009;0.10, 95% CI:0.01-0.93).<br><br>CONCLUSIONS: The abundance of Lactobacilli increased with PCOS treatment; however, the trajectory was inconsistent for each individual. Evidence of the effects of female hormone levels on the vaginal microbiome is insufficient.}, }
@article {pmid38041056, year = {2023}, author = {Simon, SA and Schmidt, K and Griesdorn, L and Soares, AR and Bornemann, TLV and Probst, AJ}, title = {Dancing the Nanopore limbo - Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {727}, pmid = {38041056}, issn = {1471-2164}, mesh = {Sequence Analysis, DNA/methods ; *Nanopores ; *Dancing ; Metagenomics/methods ; Metagenome ; Genome, Bacterial ; DNA ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {BACKGROUND: While genome-resolved metagenomics has revolutionized our understanding of microbial and genetic diversity in environmental samples, assemblies of short-reads often result in incomplete and/or highly fragmented metagenome-assembled genomes (MAGs), hampering in-depth genomics. Although Nanopore sequencing has increasingly been used in microbial metagenomics as long reads greatly improve the assembly quality of MAGs, the recommended DNA quantity usually exceeds the recoverable amount of DNA of environmental samples. Here, we evaluated lower-than-recommended DNA quantities for Nanopore library preparation by determining sequencing quality, community composition, assembly quality and recovery of MAGs.<br><br>RESULTS: We generated 27 Nanopore metagenomes using the commercially available ZYMO mock community and varied the amount of input DNA from 1000 ng (the recommended minimum) down to 1 ng in eight steps. The quality of the generated reads remained stable across all input levels. The read mapping accuracy, which reflects how well the reads match a known reference genome, was consistently high across all libraries. The relative abundance of the species in the metagenomes was stable down to input levels of 50 ng. High-quality MAGs (>&#x2009;95% completeness, &#x2264; 5% contamination) could be recovered from metagenomes down to 35 ng of input material. When combined with publicly available Illumina reads for the mock community, Nanopore reads from input quantities as low as 1 ng improved the quality of hybrid assemblies.<br><br>CONCLUSION: Our results show that the recommended DNA amount for Nanopore library preparation can be substantially reduced without any adverse effects to genome recovery and still bolster hybrid assemblies when combined with short-read data. We posit that the results presented herein will enable studies to improve genome recovery from low-biomass environments, enhancing microbiome understanding.}, }
@article {pmid38041019, year = {2023}, author = {Qi, W and Ma, T and Ji, Y and Jia, H and Sun, Q and Zhang, D}, title = {Cordymin alleviates osteoporosis induced by hindlimb unloading via regulating the gut - microelements -bone axis --for non-clinical studies.}, journal = {BMC musculoskeletal disorders}, volume = {24}, number = {1}, pages = {932}, pmid = {38041019}, issn = {1471-2474}, mesh = {Rats ; Animals ; Hindlimb Suspension/physiology ; Calcium ; *Osteoporosis/drug therapy/etiology/prevention &amp; control ; Bone and Bones/diagnostic imaging ; Bone Density/physiology ; *Bone Diseases, Metabolic ; }, abstract = {INTRODUCTION: The purpose of this study was to evaluate the protective effects of cordymin on osteoporosis induced by hindlimb unloading(HLU) in rats and whether cordymin can prevent bone loss from HLU.<br><br>MATERIALS AND METHODS: We employed the hindlimb suspension rats model to mimic physiological changes concomitant with space travel.The mechanical strength in the femoral neck,cancellous bone volume, gut microbiota structure,serum calcium and phosphorus contents, bone mineral content and bone mineral content can be changed after hindlimb unloading. Oral cordymin was administered for 4 weeks,cordymin treatment significantly increased the mechanical strength through elevated bone volume/tissue volume (BV/TV), trabecular number (Tb. N), trabecular thickness (Tb. Th) and decreased trabecular separation (Tb. Sp).<br><br>RESULTS: Importantly, 16&#xa0;S rRNA sequencing showed cordymin treatment regulated the various genera that were imbalanced in hindlimb unloading rats. At the same time,The plasma total calcium and inorganic phosphate concentrations in hindlimb unloading rats decreased and bone mineral content in the lumbar vertebrae and femur increased after treatment with cordymin.<br><br>CONCLUSION: These data indicate that the cordymin might exert bone protective effects indirectly via modulating the complex relationship between gut microbiota, microelements and bone loss.}, }
@article {pmid38040807, year = {2023}, author = {Alewel, DI and Rentschler, KM and Jackson, TW and Schladweiler, MC and Astriab-Fisher, A and Evansky, PA and Kodavanti, UP}, title = {Serum metabolome and liver transcriptome reveal acrolein inhalation-induced sex-specific homeostatic dysfunction.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {21179}, pmid = {38040807}, issn = {2045-2322}, support = {DW-089-92525001//U.S. EPA Research Participation Program/ ; }, mesh = {Rats ; Male ; Female ; Animals ; *Acrolein/toxicity ; *Transcriptome ; Rats, Inbred WKY ; Liver ; Metabolome ; }, abstract = {Acrolein, a respiratory irritant, induces systemic neuroendocrine stress. However, peripheral metabolic effects have not been examined. Male and female WKY rats were exposed to air (0 ppm) or acrolein (3.16 ppm) for 4 h, followed by immediate serum and liver tissue collection. Serum metabolomics in both sexes and liver transcriptomics in males were evaluated to characterize the systemic metabolic response. Of 887 identified metabolites, > 400 differed between sexes at baseline. An acrolein biomarker, 3-hydroxypropyl mercapturic acid, increased 18-fold in males and 33-fold in females, indicating greater metabolic detoxification in females than males. Acrolein exposure changed 174 metabolites in males but only 50 in females. Metabolic process assessment identified higher circulating free-fatty acids, glycerols, and other lipids in male but not female rats exposed to acrolein. In males, acrolein also increased branched-chain amino acids, which was linked with metabolites of nitrogen imbalance within the gut microbiome. The contribution of neuroendocrine stress was evident by increased corticosterone in males but not females. Male liver transcriptomics revealed acrolein-induced over-representation of lipid and protein metabolic processes, and pathway alterations including Sirtuin, insulin-receptor, acute-phase, and glucocorticoid signaling. In sum, acute acrolein inhalation resulted in sex-specific serum metabolomic and liver transcriptomic derangement, which may have connections to chronic metabolic-related diseases.}, }
@article {pmid38040541, year = {2023}, author = {Zhang, X and Irajizad, E and Hoffman, KL and Fahrmann, JF and Li, F and Seo, YD and Browman, GJ and Dennison, JB and Vykoukal, J and Luna, PN and Siu, W and Wu, R and Murage, E and Ajami, NJ and McQuade, JL and Wargo, JA and Long, JP and Do, KA and Lampe, JW and Basen-Engquist, KM and Okhuysen, PC and Kopetz, S and Hanash, SM and Petrosino, JF and Scheet, P and Daniel, CR}, title = {Modulating a prebiotic food source influences inflammation and immune-regulating gut microbes and metabolites: insights from the BE GONE trial.}, journal = {EBioMedicine}, volume = {}, number = {}, pages = {104873}, doi = {10.1016/j.ebiom.2023.104873}, pmid = {38040541}, issn = {2352-3964}, abstract = {BACKGROUND: Accessible prebiotic foods hold strong potential to jointly target gut health and metabolic health in high-risk patients. The BE GONE trial targeted the gut microbiota of obese surveillance patients with a history of colorectal neoplasia through a straightforward bean intervention.<br><br>METHODS: This low-risk, non-invasive dietary intervention trial was conducted at MD Anderson Cancer Center (Houston, TX, USA). Following a 4-week equilibration, patients were randomized to continue their usual diet without beans (control) or to add a daily cup of study beans to their usual diet (intervention) with immediate crossover at 8-weeks. Stool and fasting blood were collected every 4 weeks to assess the primary outcome of intra and inter-individual changes in the gut microbiome and in circulating markers and metabolites within 8 weeks. This study was registered on ClinicalTrials.gov as NCT02843425, recruitment is complete and long-term follow-up continues.<br><br>FINDINGS: Of the 55 patients randomized by intervention sequence, 87% completed the 16-week trial, demonstrating an increase on-intervention in diversity [n&#xa0;=&#xa0;48; linear mixed effect and 95% CI for inverse Simpson index: 0.16 (0.02, 0.30); p&#xa0;=&#xa0;0.02] and shifts in multiple bacteria indicative of prebiotic efficacy, including increased Faecalibacterium, Eubacterium and Bifidobacterium (all p&#xa0;<&#xa0;0.05). The circulating metabolome showed parallel shifts in nutrient and microbiome-derived metabolites, including increased pipecolic acid and decreased indole (all p&#xa0;<&#xa0;0.002) that regressed upon returning to the usual diet. No significant changes were observed in circulating lipoproteins within 8 weeks; however, proteomic biomarkers of intestinal and systemic inflammatory response, fibroblast-growth factor-19 increased, and interleukin-10 receptor-&#x3b1; decreased (p&#xa0;=&#xa0;0.01).<br><br>INTERPRETATION: These findings underscore the prebiotic and potential therapeutic role of beans to enhance the gut microbiome and to regulate host markers associated with metabolic obesity and colorectal cancer, while further emphasizing the need for consistent and sustainable dietary adjustments in high-risk patients.<br><br>FUNDING: This study was funded by the American Cancer Society.}, }
@article {pmid38040368, year = {2023}, author = {Xing, W and Gai, X and Xue, L and Chen, G}, title = {Evaluating the role of rhizosphere microbial home-field advantage in Betula luminifera adaptation to antimony mining areas.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169009}, doi = {10.1016/j.scitotenv.2023.169009}, pmid = {38040368}, issn = {1879-1026}, abstract = {It has been established that the coevolution of plants and the rhizosphere microbiome in response to abiotic stress can result in the recruitment of specific functional microbiomes. However, the potential of inoculated rhizosphere microbiomes to enhance plant fitness and the inheritance of adaptive traits in subsequent generations remains unclear. In this study, cross-inoculation trials were conducted using seeds, rhizosphere microbiome, and in situ soil collected from areas of Betula luminifera grown in both antimony mining and control sites. Compared to the control site, plants originating from mining areas exhibited stronger adaptive traits, specifically manifested as significant increases in hundred-seed weight, specific surface area, and germination rate, as well as markedly enhanced seedling survival rate and biomass. Inoculation with mining microbiomes could enhance the fitness of plants in mining sites through a "home-field advantage" while also improving the fitness of plants originating from control sites. During the initial phase of seedling development, bacteria play a crucial role in promoting growth, primarily due to their mechanisms of metal resistance and nutrient cycling. This study provided evidence that the outcomes of long-term coevolution between plants and the rhizosphere microbiome in mining areas can be passed on to future generations. Moreover, it has been demonstrated that transgenerational inheritance and rhizosphere microbiome inoculation are important factors in improving the adaptability of plants in mining areas. The findings have important implications for vegetation restoration and ecological environment improvement in mining areas.}, }
@article {pmid38040343, year = {2023}, author = {Abdi, F and Buzhor, MG and Zellweger, N and Zhi-Luo,  and Leroux, JC}, title = {pH-dependent pressure-sensitive colonic capsules for the delivery of aqueous bacterial suspensions.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jconrel.2023.11.048}, pmid = {38040343}, issn = {1873-4995}, abstract = {Microbiome-based therapies hold great promise for treating various diseases, but the efficient delivery of live bacteria to the colon remains a challenge. Furthermore, current oral formulations, such as lyophilized bacterial capsules or tablets, are produced using processes that can decrease bacterial viability. Consequently, high dosages are required to achieve efficacy. Herein, we report the design of pressure-sensitive colonic capsules for the encapsulation and delivery of aqueous suspensions of live bacteria. The capsules consisted of 2 functional thin-films (hydrophobic and enteric) of ethyl cellulose and Eudragit S100 dip-coated onto hydroxypropyl methylcellulose molds. The capsules could be loaded with aqueous media and provide protection against acidic fluids and, to some extent, oxygen diffusion, suggesting their potential suitability for delivering anaerobic bacterial strains. Disintegration and mechanical studies indicated that the capsules could withstand transit through the stomach and upper/proximal small intestinal segments and rupture in the ileum/colon. In vitro studies showed that bacterial cells (anaerobic and aerobic commensals) remained highly viable (74-98%) after encapsulation and exposure to the simulated GI tract conditions. In vivo studies with a beagle dog model revealed that 67% of the capsules opened after 3.5 h, indicating content release in the distal gastrointestinal tract. These data demonstrate that live aqueous bacterial suspensions comprised of both aerobic and anaerobic commensals can be encapsulated and in the future might be efficiently delivered to the distal gastrointestinal tract, suggesting the practical applications of these capsules in microbiome-based therapies.}, }
@article {pmid38040289, year = {2023}, author = {Mbow, FT and Akbari, A and Dopffel, N and Schneider, K and Mukherjee, S and Meckenstock, RU}, title = {Insights into the effects of anthropogenic activities on oil reservoir microbiome and metabolic potential.}, journal = {New biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.nbt.2023.11.004}, pmid = {38040289}, issn = {1876-4347}, abstract = {Microbial communities have long been observed in oil reservoirs, where the subsurface conditions are major drivers shaping their structure and functions. Furthermore, anthropogenic activities such as water flooding during oil production can affect microbial activities and community compositions in oil reservoirs through the injection of recycled produced water, often associated with biocides. However, it is still unclear to what extent the introduced chemicals and microbes influence the metabolic potential of the subsurface microbiome. Here we investigated an onshore oilfield in Germany (Field A) that undergoes secondary oil production along with biocide treatment to prevent souring and microbially induced corrosion (MIC). With the integrated approach of 16S rRNA gene amplicon and shotgun metagenomic sequencing of water-oil samples from 4 production wells and 1 injection well, we found differences in microbial community structure and metabolic functions. In the injection water samples, amplicon sequence variants (ASVs) belonging to families such as Halanaerobiaceae, Ectothiorhodospiraceae, Hydrogenophilaceae, Halobacteroidaceae, Desulfohalobiaceae, and Methanosarcinaceae were dominant, while in the production water samples, ASVs of families such as Thermotogaceae, Nitrospiraceae, Petrotogaceae, Syntrophaceae, Methanobacteriaceae, and Thermoprotei were also dominant. The metagenomic analysis of the injection water sample revealed the presence of C1-metabolism, namely, genes involved in formaldehyde oxidation. Our analysis revealed that the microbial community structure of the production water samples diverged slightly from that of injection water samples. Additionally, a metabolic potential for oxidizing the applied biocide clearly occurred in the injection water samples indicating an adaptation and buildup of degradation capacity or resistance against the added biocide.}, }
@article {pmid38040073, year = {2023}, author = {Duffy, EP and Bachtell, RK and Ehringer, MA}, title = {Opioid trail: Tracking contributions to opioid use disorder from host genetics to the gut microbiome.}, journal = {Neuroscience and biobehavioral reviews}, volume = {156}, number = {}, pages = {105487}, doi = {10.1016/j.neubiorev.2023.105487}, pmid = {38040073}, issn = {1873-7528}, abstract = {Opioid use disorder (OUD) is a worldwide public health crisis with few effective treatment options. Traditional genetics and neuroscience approaches have provided knowledge about biological mechanisms that contribute to OUD-related phenotypes, but the complexity and magnitude of effects in the brain and body remain poorly understood. The gut-brain axis has emerged as a promising target for future therapeutics for several psychiatric conditions, so characterizing the relationship between host genetics and the gut microbiome in the context of OUD will be essential for development of novel treatments. In this review, we describe evidence that interactions between host genetics, the gut microbiome, and immune signaling likely play a key role in mediating opioid-related phenotypes. Studies in humans and model organisms consistently demonstrated that genetic background is a major determinant of gut microbiome composition. Furthermore, the gut microbiome is susceptible to environmental influences such as opioid exposure. Additional work focused on gene by microbiome interactions will be necessary to gain improved understanding of their effects on OUD-related behaviors.}, }
@article {pmid38039945, year = {2023}, author = {Liu, YN and Bairoliya, S and Zaiden, N and Cao, B}, title = {Establishment of plastic-associated microbial community from superworm gut microbiome.}, journal = {Environment international}, volume = {183}, number = {}, pages = {108349}, doi = {10.1016/j.envint.2023.108349}, pmid = {38039945}, issn = {1873-6750}, abstract = {Gut microbial communities of plastic-munching worms provide novel insights for the development of plastic-processing biotechnologies. Considering the complexity of worm maintenance and the gut microbial communities, it is challenging to apply the worms directly in plastic processing. Harnessing the power of microbial communities derived from the worm gut microbiomes in vitro may enable a promising bioprocess for plastic degradation. Here, we established stable and reproducible plastic-associated biofilm communities derived from the gut microbiome of a superworm, Zophobas atratus, through a two-stage enrichment process: feeding with plastics (HDPE, PP, and PS) and in vitro incubation of gut microbiomes obtained from the plastic-fed worms. Plastic feeding exhibited marginal influence on bacterial diversity but substantially changed the relative abundance of different bacterial groups, and intriguingly, enriched potential plastic degraders. More prominent shifts of microbial communities were observed during the in vitro incubation of the gut microbiomes. Taxa containing plastic-degrading strains were further enriched, while other taxa represented by lactic acid bacteria were depleted. Additionally, the plastic characterization confirmed the degradation of the incubated plastics by the plastic-associated microbial communities. Community functional inference for both gene abundance and community phenotype suggested that the in vitro incubation enhanced plastic-degrading potential. Deterministic ecological effects, in particular, selection processes, were identified as the main driving force of the observed community shifts. Our findings provide novel insights into plastic-munching-worm-inspired bioprocessing of plastic wastes.}, }
@article {pmid38039804, year = {2023}, author = {Duan, B and Gan, M and Xu, Z and Chen, WX}, title = {Tonsil microbiome in pediatric patients with post tonsillectomy hemorrhage for tonsillar hypertrophy.}, journal = {International journal of pediatric otorhinolaryngology}, volume = {176}, number = {}, pages = {111788}, doi = {10.1016/j.ijporl.2023.111788}, pmid = {38039804}, issn = {1872-8464}, abstract = {OBJECTIVE: This study aimed to compare the tonsillar microbiota between post tonsillectomy patients with bleeding and without bleeding, and to investigate the potential role of tonsillar microbiota in the development of post-tonsillectomy hemorrhage (PTH).<br><br>METHODS: Nineteen tonsillar tissues from PTH patients and 21 tissues from control patients were collected. Metagenomic sequencing was used to compare the microbiota in PTH and control groups. Alpha diversity indices were used to compare the richness and evenness of the microbiota between the two groups. PCoA and NMDS analyses were used to evaluate beta diversity. LDA analysis was conducted to identify significantly abundant genera.<br><br>RESULTS: No significant difference in alpha diversity indices was found between PTH and control patients. The dominant bacteria in the tonsillar microbiota were Haemophilus, Streptococcus, and Fusobacterium. PCoA and NMDS analyses showed significant differences in beta diversity between PTH and control patients. PTH patients had a significantly higher relative abundance of Neisseria, Capnocytophaga, and Veillonella. Capnocytophaga was also identified as a significantly abundant genus by LDA analysis.<br><br>CONCLUSION: This study demonstrates that there is a difference in the tonsillar microbiota between PTH and control patients. The results suggest that Neisseria, Capnocytophaga, and Veillonella may be associated with the development of PTH. These findings provide new insights into the potential role of the tonsillar microbiota in the development of PTH, and may help to develop new strategies for preventing and treating this potentially life-threatening complication.}, }
@article {pmid38039494, year = {2023}, author = {Gungor, O and Hasbal, NB and Alaygut, D}, title = {Trimethylamine N-oxide and kidney diseases: what do we know?.}, journal = {Jornal brasileiro de nefrologia}, volume = {}, number = {}, pages = {}, doi = {10.1590/2175-8239-JBN-2023-0065en}, pmid = {38039494}, issn = {2175-8239}, abstract = {In the human gut, there is a metabolically active microbiome whose metabolic products reach various organs and are used in the physiological activities of the body. When dysbiosis of intestinal microbial homeostasis occurs, pathogenic metabolites may increase and one of them is trimethyl amine-N-oxide (TMAO). TMAO is thought to have a role in the pathogenesis of insulin resistance, diabetes, hyperlipidemia, atherosclerotic heart diseases, and cerebrovascular events. TMAO level is also associated with renal inflammation, fibrosis, acute kidney injury, diabetic kidney disease, and chronic kidney disease. In this review, the effect of TMAO on various kidney diseases is discussed.}, }
@article {pmid38038731, year = {2023}, author = {Jørgensen, AB and Jonsson, I and Friis-Hansen, L and Brandstrup, B}, title = {Collagenase-producing bacteria are common in anastomotic leakage after colorectal surgery: a systematic review.}, journal = {International journal of colorectal disease}, volume = {38}, number = {1}, pages = {275}, pmid = {38038731}, issn = {1432-1262}, mesh = {Humans ; Anastomotic Leak/etiology ; *Colorectal Surgery/adverse effects ; *Digestive System Surgical Procedures ; Collagenases ; Bacteria ; }, abstract = {PURPOSE: Some gut bacteria can produce enzymes (collagenases) that can break down collagen in the intestinal wall. This could be a part of the pathophysiology of anastomotic leakage (AL). This systematic review aimed to investigate if such bacteria were present more frequently in AL patients versus non-AL patients following colorectal surgery.<br><br>METHODS: This systematic review was reported according to the PRISMA and AMSTAR guidelines. Before the literature search, a study protocol was registered at PROSPERO (CRD42022363454). We searched PubMed, EMBASE, Google Scholar, and Cochrane CENTRAL on April 9[th], 2023, for randomized and observational human studies of AL following colorectal surgery with information on gastrointestinal bacteria. The primary outcome was bacteria with the potential to produce collagenase. The risk of bias was assessed with the Newcastle-Ottawa Scale, as all studies were observational.<br><br>RESULTS: We included 15 studies, with a total of 52,945 patients, of which 1,747 had AL, and bacteriological information from feces, mucosa, the resected specimen, or drain fluid was presented. In 10 of the 15 studies, one or more collagenase-producing bacteria were identified in the patients with AL. Neither the bacteria nor the collagenase production were quantified in any of the studies. The studies varied greatly in terms of sample material, analytical method, and time of collection. Studies using DNA sequencing methods did not report findings of collagenase-producing bacteria.<br><br>CONCLUSION: Collagenase-producing bacteria are more common in patients with AL following colorectal surgery than in patients without AL, but the significance is unclear. From the current studies, it is not possible to determine the pathogenicity of the individual gut bacteria.}, }
@article {pmid38038696, year = {2023}, author = {Pogoda, CS and Keepers, KG and Reinert, S and Talukder, ZI and Smart, BC and Attia, Z and Corwin, JA and Money, KL and Collier-Zans, ECE and Underwood, W and Gulya, TJ and Quandt, CA and Kane, NC and Hulke, BS}, title = {Heritable differences in abundance of bacterial rhizosphere taxa are correlated with fungal necrotrophic pathogen resistance.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.17218}, pmid = {38038696}, issn = {1365-294X}, support = {3060-21000-039//USDA-ARS CRIS projects/ ; 3060-21000-043//USDA-ARS CRIS projects/ ; 5442-21220-024//USDA-ARS CRIS projects/ ; 2019077//NSF MRI/ ; FI-577-2018//BARD, United States - Israel Binational Agricultural Research and Development Fund/ ; }, abstract = {Host-microbe interactions are increasingly recognized as important drivers of organismal health, growth, longevity and community-scale ecological processes. However, less is known about how genetic variation affects hosts' associated microbiomes and downstream phenotypes. We demonstrate that sunflower (Helianthus annuus) harbours substantial, heritable variation in microbial communities under field conditions. We show that microbial communities co-vary with heritable variation in resistance to root infection caused by the necrotrophic pathogen Sclerotinia sclerotiorum and that plants grown in autoclaved soil showed almost complete elimination of pathogen resistance. Association mapping suggests at least 59 genetic locations with effects on both microbial relative abundance and Sclerotinia resistance. Although the genetic architecture appears quantitative, we have elucidated previously unexplained genetic variation for resistance to this pathogen. We identify new targets for plant breeding and demonstrate the potential for heritable microbial associations to play important roles in defence in natural and human-altered environments.}, }
@article {pmid38038446, year = {2023}, author = {Härer, A and Rennison, DJ}, title = {The effects of host ecology and phylogeny on gut microbiota (non)parallelism across birds and mammals.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0044223}, doi = {10.1128/msphere.00442-23}, pmid = {38038446}, issn = {2379-5042}, abstract = {What are the roles of determinism and contingency in evolution? The paleontologist and evolutionary biologist Stephen J. Gould raised this question in his famous thought experiment of "replaying life's tape." Settings where independent lineages have repeatedly adapted to similar ecological niches (i.e., parallel evolution) are well suited to address this question. Here, we quantified whether repeated ecological shifts across 53 mammalian and 50 avian host species are associated with parallel gut microbiota changes. Our results indicate that parallel shifts in host diet are associated with greater gut microbiota parallelism (i.e., more deterministic). While further research will be necessary to obtain a comprehensive picture of the circumstances under which deterministic gut microbiota changes might be expected, our study can be instrumental in motivating the use of more quantitative methods in microbiota research. This, in turn, can help us better understand microbiota dynamics during adaptive evolution of their hosts.}, }
@article {pmid38038385, year = {2023}, author = {Li, CC and Hsu, WF and Chiang, PC and Kuo, MC and Wo, AM and Tseng, YJ}, title = {Characterization of markers, functional properties, and microbiome composition in human gut-derived bacterial extracellular vesicles.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2288200}, doi = {10.1080/19490976.2023.2288200}, pmid = {38038385}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Microbiota/genetics ; Feces/microbiology ; Bacteria/genetics ; *Extracellular Vesicles ; RNA, Ribosomal, 16S/genetics ; DNA ; }, abstract = {Past studies have confirmed the etiologies of bacterial extracellular vesicles (BEVs) in various diseases, including inflammatory bowel disease (IBD) and colorectal cancer (CRC). This study aimed to investigate the characteristics of stool-derived bacterial extracellular vesicles (stBEVs) and discuss their association with stool bacteria. First, three culture models - gram-positive (G+)BcBEVs (from B.coagulans), gram-negative (G-)EcBEVs (from E.coli), and eukaryotic cell-derived EVs (EEV, from Colo205 cell line) - were used to benchmark various fractions of stEVs separated from optimized density gradient approach (DG). As such, WB, TEM, NTA, and functional assays, were utilized to analyze properties and distribution of EVs in cultured and stool samples. Stool samples from healthy individuals were interrogated using the approaches developed. Results demonstrated successful separation of most stBEVs (within DG fractions 8&amp;9) from stEEVs (within DG fractions 5&amp;6). Data also suggest the presence of stBEV DNA within vesicles after extraction of BEV DNA and DNase treatment. Metagenomic analysis from full-length (FL) region sequencing results confirmed significant differences between stool bacteria and stBEVs. Significantly, F8&amp;9 and the pooled sample (F5-F9) exhibited a similar microbial composition, indicating that F8&amp;9 were enriched in most stBEV species, primarily dominated by Firmicutes (89.6%). However, F5&amp;6 and F7 still held low-density BEVs with a significantly higher proportion of Proteobacteria (20.5% and 40.7%, respectively) and Bacteroidetes (24% and 13.7%, respectively), considerably exceeding the proportions in stool and F8&amp;9. Importantly, among five healthy individuals, significant variations were observed in the gut microbiota composition of their respective stBEVs, indicating the potential of stBEVs as a target for personalized medicine and research.}, }
@article {pmid38037712, year = {2023}, author = {Gao, M and Xiong, C and Tsui, CKM and Cai, L}, title = {Pathogen invasion increases the abundance of predatory protists and their prey associations in the plant microbiome.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.17228}, pmid = {38037712}, issn = {1365-294X}, support = {32330002//National Natural Science Foundation of China/ ; }, abstract = {Soil and plant-associated protistan communities play a key role in shaping bacterial and fungal communities, primarily through their function as top-down predators. However, our understanding of how pathogen invasion influences these protistan communities and their relationships with bacterial and fungal communities remains limited. Here, we studied the protistan communities along the soil-plant continuum of healthy chilli peppers and those affected by Fusarium wilt disease (FWD), and integrated bacterial and fungal community data from our previous research. Our research showed that FWD was associated with a significant enrichment of phagotrophic protists in roots, and also increased the proportion and connectivity of these protists (especially Cercozoa and Ciliophora) in both intra- and inter-kingdom networks. Furthermore, the microbiome of diseased plants not only showed a higher relative abundance of functional genes related to bacterial anti-predator responses than healthy plants, but also contained a greater abundance of metagenome-assembled genomes with functional traits involved in this response. The increased microbial inter-kingdom associations between bacteria and protists, coupled with the notable bacterial anti-predator feedback in the microbiome of diseased plants, suggest that FWD may catalyse the associations between protists and their microbial prey. These findings highlight the potential role of predatory protists in influencing microbial assembly and functionality through top-down forces under pathogenic stress.}, }
@article {pmid38037395, year = {2023}, author = {Nguyen, PN and Rehan, SM}, title = {Wild bee and pollen microbiomes across an urban-rural divide.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiad158}, pmid = {38037395}, issn = {1574-6941}, abstract = {Wild pollinators and their microbiota are sensitive to land use changes from anthropogenic activities that disrupt landscape and environmental features. As urbanization and agriculture affect bee habitats, human led disturbances are driving changes in bee microbiomes, potentially leading to dysbiosis detrimental to bee fitness. This study examines the bacterial, fungal, and plant compositions of the small carpenter bee, Ceratina calcarata, and its pollen provisions across an urban-rural divide. We performed metabarcoding of C. calcarata and provisions in Toronto by targeting the 16S rRNA, ITS, and rbcL regions. Despite similar plant composition and diversity across bees and their provisions, there was a greater microbial diversity in pollen provisions than in bees. By characterizing the differences in land use, climate, and pesticide residues that differentiate urban and rural landscapes, we find that urban areas support elevated levels of microbial diversity and more complex networks between microbes and plants than rural areas. However, urban areas may lead to lower relative abundances of known beneficial symbionts and increased levels of pathogens, such as Ascosphaera and Alternaria fungi. Further, rural pollen provisions indicate elevated pesticide residues that may dysregulate symbiosis. As anthropogenic activities continue to alter land use, ever changing environments threaten microbiota crucial in maintaining bee health.}, }
@article {pmid38037191, year = {2023}, author = {Santiago, P and Quinn, KP and Chen, J and Friton, JJ and Rypstra, CR and Kashyap, PC and Raffals, LE}, title = {Altered Bile Acid and Pouch Microbiota Composition in Patients With Chronic Pouchitis.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izad288}, pmid = {38037191}, issn = {1536-4844}, support = {/TR/NCATS NIH HHS/United States ; /NH/NIH HHS/United States ; }, abstract = {BACKGROUND: Patients with ulcerative colitis and total abdominal proctocolectomy with ileal pouch-anal anastomosis have a 50% risk of pouchitis and a 5% to 10% risk of chronic pouchitis.<br><br>AIMS: The goal of the study was to compare pouch microbiota and stool bile acid composition in patients with chronic pouchitis, chronic pouchitis and primary sclerosing cholangitis, and normal pouch.<br><br>METHODS: Patients with ulcerative colitis and ileal pouch-anal anastomosis were recruited from March 20, 2014, to August 6, 2019, and categorized into normal pouch, chronic pouchitis, and chronic pouchitis/primary sclerosing cholangitis groups. Stool samples were subjected to bile acid quantification and 16S rRNA gene sequencing. Statistical comparisons of absolute bile acid abundance and pouch microbiota &#x3b1;-diversity, &#x3b2;-diversity, and taxa abundance were performed among the patient groups.<br><br>RESULTS: A total of 51 samples were analyzed. Both &#x3b1;-diversity (P&#x2005;=&#x2005;.01, species richness) and &#x3b2;-diversity (P&#x2005;=&#x2005;.001) significantly differed among groups. Lithocholic acid was significantly lower in patients with chronic pouchitis/primary sclerosing cholangitis than in those with chronic pouchitis (P&#x2005;=&#x2005;.01) or normal pouch (P&#x2005;=&#x2005;.03). Decreased &#x3b1;-diversity was associated with an increased primary to secondary bile acid ratio (P&#x2005;=&#x2005;.002), which was also associated with changes in &#x3b2;-diversity (P&#x2005;=&#x2005;.006).<br><br>CONCLUSIONS: Pouch microbiota &#x3b1;- and &#x3b2;-diversity differed among patients with normal pouch, chronic pouchitis, and chronic pouchitis/primary sclerosing cholangitis. Lithocholic acid level and primary to secondary bile acid ratio were highly associated with pouch microbiota richness, structure, and composition. These findings emphasize the associations between pouch microbiota and bile acid composition in dysbiosis and altered metabolism, suggesting that secondary bile acids are decreased in chronic pouchitis.}, }
@article {pmid38037145, year = {2023}, author = {Nishiwaki, R and Imoto, I and Oka, S and Yasuma, T and Fujimoto, H and D'Alessandro-Gabazza, CN and Toda, M and Kobayashi, T and Osamu, H and Fujibe, K and Nishikawa, K and Hamaguchi, T and Sugimasa, N and Noji, M and Ito, Y and Takeuchi, K and Cann, I and Inoue, Y and Kato, T and Gabazza, EC}, title = {Elevated plasma and bile levels of corisin, a microbiota-derived proapoptotic peptide, in patients with severe acute cholangitis.}, journal = {Gut pathogens}, volume = {15}, number = {1}, pages = {59}, pmid = {38037145}, issn = {1757-4749}, support = {2023//Takeda Foundation/ ; 2023//Takeda Foundation/ ; Grant No 23K7651//Japan Science and Technology Agency/ ; }, abstract = {BACKGROUND: Acute cholangitis is a severe, life-threatening infection of the biliary system that requires early diagnosis and treatment. The Tokyo Guidelines recommend a combination of clinical, laboratory, and imaging findings for diagnosis and severity assessment, but there are still challenges in identifying severe cases that need immediate intervention. The microbiota and its derived products have been implicated in the pathogenesis of acute cholangitis. Corisin is a microbiome-derived peptide that induces cell apoptosis, acute tissue injury, and inflammation. This study aimed to evaluate the potential of plasma and bile corisin as a biomarker of acute cholangitis.<br><br>METHODS: Forty patients with acute cholangitis associated with choledocholithiasis or malignant disease were enrolled. Nine patients without acute cholangitis were used as controls. Corisin was measured by enzyme immunoassays in plasma and bile samples. Patients were classified into severe and non-severe groups. The associations of plasma and bile corisin with the clinical grade of acute cholangitis and other parameters were analyzed by univariate and multivariate regression analysis.<br><br>RESULTS: Plasma and bile corisin levels were significantly higher in patients with acute cholangitis than in controls. Patients with severe acute cholangitis had significantly higher plasma and bile corisin levels than those with non-severe form of the disease. Bile corisin level was significantly correlated with markers of inflammation, coagulation, fibrinolysis, and renal function. Univariate analysis revealed a significant association of bile corisin but a weak association of plasma corisin with the clinical grade of acute cholangitis. In contrast, multivariate analysis showed a significant relationship between plasma corisin level and the disease clinical grade. The receiver operating characteristic curve analysis showed low sensitivity but high specificity for plasma and bile corisin to detect the severity of acute cholangitis. The plasma and bile corisin sensitivity was increased when serum C-reactive protein level was included in the receiver operating characteristic curve analysis.<br><br>CONCLUSIONS: Overall, these findings suggest that plasma and bile corisin levels may be useful biomarkers for diagnosing and monitoring acute cholangitis and that corisin may play a role in the pathophysiology of the disease by modulating inflammatory, coagulation and renal pathways.}, }
@article {pmid38037123, year = {2023}, author = {Medeiros, MC and The, S and Bellile, E and Russo, N and Schmitd, L and Danella, E and Singh, P and Banerjee, R and Bassis, C and Murphy, GR and Sartor, MA and Lombaert, I and Schmidt, TM and Eisbruch, A and Murdoch-Kinch, CA and Rozek, L and Wolf, GT and Li, G and Chen, GY and D'Silva, NJ}, title = {Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {268}, pmid = {38037123}, issn = {2049-2618}, support = {DE027551/DE/NIDCR NIH HHS/United States ; CA250214/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Mouth Neoplasms/therapy ; Longitudinal Studies ; *Carcinoma, Squamous Cell ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Saliva/microbiology ; Bacteria/genetics ; Calcium-Binding Proteins ; DNA-Binding Proteins ; Tumor Suppressor Proteins ; }, abstract = {BACKGROUND: Oral squamous cell carcinoma (SCC) is associated with oral microbial dysbiosis. In this unique study, we compared pre- to post-treatment salivary microbiome in patients with SCC by 16S rRNA gene sequencing and examined how microbiome changes correlated with the expression of an anti-microbial protein.<br><br>RESULTS: Treatment of SCC was associated with a reduction in overall bacterial richness and diversity. There were significant changes in the microbial community structure, including a decrease in the abundance of Porphyromonaceae and Prevotellaceae and an increase in Lactobacillaceae. There were also significant changes in the microbial community structure before and after treatment with chemoradiotherapy, but not with surgery alone. In patients treated with chemoradiotherapy alone, several bacterial populations were differentially abundant between responders and non-responders before and after therapy. Microbiome changes were associated with a change in the expression of DMBT1, an anti-microbial protein in human saliva. Additionally, we found that salivary DMBT1, which increases after treatment, could serve as a post-treatment salivary biomarker that links to microbial changes. Specifically, post-treatment increases in human salivary DMBT1 correlated with increased abundance of Gemella spp., Pasteurellaceae spp., Lactobacillus spp., and Oribacterium spp. This is the first longitudinal study to investigate treatment-associated changes (chemoradiotherapy and surgery) in the oral microbiome in patients with SCC along with changes in expression of an anti-microbial protein in saliva.<br><br>CONCLUSIONS: The composition of the oral microbiota may predict treatment responses; salivary DMBT1 may have a role in modulating the oral microbiome in patients with SCC. After completion of treatment, 6 months after diagnosis, patients had a less diverse and less rich oral microbiome. Leptotrichia was a highly prevalent bacteria genus associated with disease. Expression of DMBT1 was higher after treatment and associated with microbiome changes, the most prominent genus being Gemella Video Abstract.}, }
@article {pmid38037013, year = {2023}, author = {Liu, Z and Chen, P and Luo, L and Liu, Q and Shi, H and Yang, X}, title = {Causal effects of gut microbiome on endometriosis: a two-sample mendelian randomization study.}, journal = {BMC women's health}, volume = {23}, number = {1}, pages = {637}, pmid = {38037013}, issn = {1472-6874}, support = {208195823065//Guangdong Provincial Natural Science Foundation Project General Project/ ; }, abstract = {BACKGROUND: Previous studies have shown observational associations between the gut microbiota and endometriosis; however, the causal nature of such associations remains unclear. This study aimed to analyze the genetic causal relationship between the two.<br><br>METHODS: A gut microbiome genome-wide association study conducted by the MiBioGen consortium was used as exposure data, and summary statistics of endometriosis were obtained from the FinnGen consortium R8 release data. Inverse variance weighted, MR-Egger, weighted median, weighted model, and simple model analyses were applied to examine the causal relationship, and sensitivity analyses were conducted to validate the robustness of the results.<br><br>RESULTS: The results showed that, out of 211 gut microbiome taxa, Clostridiales_vadin_BB60_group, Oxalobacteraceae, Desulfovibrio, Haemophilus, and Holdemania had protective effects on endometriosis, while Porphyromonadaceae and Anaerotruncus might contribute to the development of endometriosis. Heterogeneity and pleiotropy analyses confirmed the robustness of the results.<br><br>CONCLUSION: The two-sample Mendelian randomization analysis conducted in this study identified specific intestinal flora with a causal relationship with endometriosis at the genetic level, offering new insights into the gut microbiota-mediated development mechanism of endometriosis.}, }
@article {pmid38036970, year = {2023}, author = {Martins, BR and Siani, R and Treder, K and Michałowska, D and Radl, V and Pritsch, K and Schloter, M}, title = {Cultivar-specific dynamics: unravelling rhizosphere microbiome responses to water deficit stress in potato cultivars.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {377}, pmid = {38036970}, issn = {1471-2180}, abstract = {BACKGROUND: Growing evidence suggests that soil microbes can improve plant fitness under drought. However, in potato, the world's most important non-cereal crop, the role of the rhizosphere microbiome under drought has been poorly studied. Using a cultivation independent metabarcoding approach, we examined the rhizosphere microbiome of two potato cultivars with different drought tolerance as a function of water regime (continuous versus reduced watering) and manipulation of soil microbial diversity (i.e., natural (NSM), vs. disturbed (DSM) soil microbiome).<br><br>RESULTS: Water regime and soil pre-treatment showed a significant interaction with bacterial community composition of the sensitive (HERBST) but not the resistant cultivar (MONI). Overall, MONI had a moderate response to the treatments and its rhizosphere selected Rhizobiales under reduced watering in NSM soil, whereas Bradyrhizobium, Ammoniphilus, Symbiobacterium and unclassified Hydrogenedensaceae in DSM soil. In contrast, HERBST response to the treatments was more pronounced. Notably, in NSM soil treated with reduced watering, the root endophytic fungus Falciphora and many Actinobacteriota members (Streptomyces, Glycomyces, Marmoricola, Aeromicrobium, Mycobacterium and others) were largely represented. However, DSM soil treatment resulted in no fungal taxa and fewer enrichment of these Actinobacteriota under reduced watering. Moreover, the number of bacterial core amplicon sequence variants (core ASVs) was more consistent in MONI regardless of soil pre-treatment and water regimes as opposed to HERBST, in which a marked reduction of core ASVs was observed in DSM soil.<br><br>CONCLUSIONS: Besides the influence of soil conditions, our results indicate a strong cultivar-dependent relationship between the rhizosphere microbiome of potato cultivars and their capacity to respond to perturbations such as reduced soil moisture. Our study highlights the importance of integrating soil conditions and plant genetic variability as key factors in future breeding programs aiming to develop drought resistance in a major food crop like potato. Elucidating the molecular mechanisms how plants recruit microbes from soil which help to mitigate plant stress and to identify key microbial taxa, which harbour the respective traits might therefore be an important topic for future research.}, }
@article {pmid38036944, year = {2023}, author = {Kulkarni, DH and Rusconi, B and Floyd, AN and Joyce, EL and Talati, KB and Kousik, H and Alleyne, D and Harris, DL and Garnica, L and McDonough, R and Bidani, SS and Kulkarni, HS and Newberry, EP and McDonald, KG and Newberry, RD}, title = {Gut microbiota induces weight gain and inflammation in the gut and adipose tissue independent of manipulations in diet, genetics, and immune development.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2284240}, doi = {10.1080/19490976.2023.2284240}, pmid = {38036944}, issn = {1949-0984}, abstract = {Obesity and the metabolic syndrome are complex disorders resulting from multiple factors including genetics, diet, activity, inflammation, and gut microbes. Animal studies have identified roles for each of these, however the contribution(s) specifically attributed to the gut microbiota remain unclear, as studies have used combinations of genetically altered mice, high fat diet, and/or colonization of germ-free mice, which have an underdeveloped immune system. We investigated the role(s) of the gut microbiota driving obesity and inflammation independent of manipulations in diet and genetics in mice with fully developed immune systems. We demonstrate that the human obese gut microbiota alone was sufficient to drive weight gain, systemic, adipose tissue, and intestinal inflammation, but did not promote intestinal barrier leak. The obese microbiota induced gene expression promoting caloric uptake/harvest but was less effective at inducing genes associated with mucosal immune responses. Thus, the obese gut microbiota is sufficient to induce weight gain and inflammation.}, }
@article {pmid38036921, year = {2023}, author = {Gallardo-Becerra, L and Cervantes-Echeverría, M and Cornejo-Granados, F and Vazquez-Morado, LE and Ochoa-Leyva, A}, title = {Perspectives in Searching Antimicrobial Peptides (AMPs) Produced by the Microbiota.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {8}, pmid = {38036921}, issn = {1432-184X}, support = {Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; PAPIIT UNAM (IN219723)//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; PAPIIT UNAM (IN219723)//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; PAPIIT UNAM (IN219723)//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; PAPIIT UNAM (IN219723)//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; PAPIIT UNAM (IN219723)//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; }, abstract = {Changes in the structure and function of the microbiota are associated with various human diseases. These microbial changes can be mediated by antimicrobial peptides (AMPs), small peptides produced by the host and their microbiota, which play a crucial role in host-bacteria co-evolution. Thus, by studying AMPs produced by the microbiota (microbial AMPs), we can better understand the interactions between host and bacteria in microbiome homeostasis. Additionally, microbial AMPs are a new source of compounds against pathogenic and multi-resistant bacteria. Further, the growing accessibility to metagenomic and metatranscriptomic datasets presents an opportunity to discover new microbial AMPs. This review examines the structural properties of microbiota-derived AMPs, their molecular action mechanisms, genomic organization, and strategies for their identification in any microbiome data as well as experimental testing. Overall, we provided a comprehensive overview of this important topic from the microbial perspective.}, }
@article {pmid38036651, year = {2023}, author = {Chhina, MS}, title = {Are e-cigarettes a safer alternative to reduce incidences of oral cancer?.}, journal = {Evidence-based dentistry}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41432-023-00956-7}, pmid = {38036651}, issn = {1476-5446}, abstract = {INTRODUCTION: The rapid increase in the use of electronic nicotine delivery systems (ENDS), such as e-cigarettes and vape pens, has raised concerns about their potential impact on oral health and the risk of oral cancer. Despite their popularity and claims of being a safer alternative to traditional smoking, there is a lack of conclusive evidence regarding the detrimental effects of vaping. ENDS were initially introduced as a safer option for smokers, attracting both traditional smokers and adolescents due to appealing flavours. These devices use a battery-powered heating element to aerosolise a liquid containing nicotine, flavourings, formaldehyde, glycerol, and heavy metals. However, the variability in product composition and design makes it challenging to establish reliable toxicity profiles. This commentary aims to provide an overview of the existing evidence to inform oral and maxillofacial surgery (OMFS) practitioners about the potential risks associated with vaping on oral health and cancer.<br><br>DATA SOURCES: Data was extracted from ten recent studies, which included systematic reviews, meta-analyses, literature reviews, cross-sectional analyses, and in-vitro studies.<br><br>RESULTS: While e-cigarettes have fewer carcinogens than traditional cigarettes, concerns remain about their potential for DNA damage. Reported oral symptoms related to e-cigarette use include dry mouth, irritation, pain, oral ulcers, nicotine-related conditions, and accidents resulting from device malfunctions. ENDS exposure has been linked to oral health issues like dysbiosis, inflammation, periodontal disease, and alterations in the oral microbiome. In-vitro studies have shown that e-cigarettes can induce DNA damage, oxidative stress, and genotoxicity in oral cells. Although direct causality between e-cigarettes and oral cancer remains unclear, there are case reports of oral cancer in heavy e-cigarette users without other traditional risk factors. Additionally, some ENDS components, such as formaldehyde and acetaldehyde, are known human carcinogens, potentially posing a nasopharyngeal cancer risk. ENDS use may increase chemotherapy resistance and alter immune-related gene expression, potentially facilitating HPV-16 infection. Moreover, there is concern that ENDS use could lead to future tobacco smoking among adolescents. The variability in ENDS products further complicates assessing their oral health effects.<br><br>CONCLUSIONS: Based on current evidence, ENDS should not be considered 'safe'. The authors recommend documenting ENDS consumption and emphasise the need for extensive research to better understand their effects on oral cavity tissues. Clinicians should remain vigilant and educate patients about the potential risks associated with vaping to make informed decisions about their oral health.}, }
@article {pmid38036587, year = {2023}, author = {Hong, YM and Lee, J and Cho, DH and Jeon, JH and Kang, J and Kim, MG and Lee, S and Kim, JK}, title = {Predicting preterm birth using machine learning techniques in oral microbiome.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {21105}, pmid = {38036587}, issn = {2045-2322}, abstract = {Preterm birth prediction is essential for improving neonatal outcomes. While many machine learning techniques have been applied to predict preterm birth using health records, inflammatory markers, and vaginal microbiome data, the role of prenatal oral microbiome remains unclear. This study aimed to compare oral microbiome compositions between a preterm and a full-term birth group, identify oral microbiome associated with preterm birth, and develop a preterm birth prediction model using machine learning of oral microbiome compositions. Participants included singleton pregnant women admitted to Jeonbuk National University Hospital between 2019 and 2021. Subjects were divided into a preterm and a full-term birth group based on pregnancy outcomes. Oral microbiome samples were collected using mouthwash within 24 h before delivery and 16S ribosomal RNA sequencing was performed to analyze taxonomy. Differentially abundant taxa were identified using DESeq2. A random forest classifier was applied to predict preterm birth based on the oral microbiome. A total of 59 women participated in this study, with 30 in the preterm birth group and 29 in the full-term birth group. There was no significant difference in maternal clinical characteristics between the preterm and the full-birth group. Twenty-five differentially abundant taxa were identified, including 22 full-term birth-enriched taxa and 3 preterm birth-enriched taxa. The random forest classifier achieved high balanced accuracies (0.765 ± 0.071) using the 9 most important taxa. Our study identified 25 differentially abundant taxa that could differentiate preterm and full-term birth groups. A preterm birth prediction model was developed using machine learning of oral microbiome compositions in mouthwash samples. Findings of this study suggest the potential of using oral microbiome for predicting preterm birth. Further multi-center and larger studies are required to validate our results before clinical applications.}, }
@article {pmid38036562, year = {2023}, author = {Sagara, K and Kataoka, S and Yoshida, A and Ansai, T}, title = {The effects of exposure to O2- and HOCl-nanobubble water on human salivary microbiota.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {21125}, pmid = {38036562}, issn = {2045-2322}, support = {19K19317//Japan Society for the Promotion of Science/ ; }, abstract = {Nanobubbles of gas remain dissolved in water for longer periods than ordinary bubbles, and exhibit unique physicochemical and biological properties. As a result, nanobubble water (NBW) is finding widespread use many applications, such as cleaning in the industry and purification of lake water. The ozone NBW (O3-NBW), in particular, has been used in clinical dentistry; however, it has several disadvantages, including the instability of ozone, which is spontaneously converted to molecular oxygen (O3 to O2), and its broad range of antibacterial activity, which can disrupt the oral microbiota. Therefore, the use of NBW in dental medicine requires greater evaluation. Here, we examined the effects of oxygen and hypochlorite NBW (O2-NBW and HOCl-NBW, respectively) on the microbiota in human saliva in 16 male patients (35-75 years old; median: 53.5 years) using multiple assays, including next generation sequencing analysis. 16S rRNA gene sequencing revealed no significant changes in both alpha-diversity and beta-diversity. Principal Coordinate Analysis (PCoA) revealed two subclusters in both unweighted and weighted UniFrac distances. Overall, the results revealed that HOCl-NBW exposure of saliva may lead to inhibition or delay in oral biofilm formation while maintaining the balance of the oral microbiome. These results can lead to the development of a novel type of mouthrinse for prevention of oral infectious diseases.}, }
@article {pmid38036453, year = {2023}, author = {Ng, AC and Choudhary, A and Barrett, KT and Gavrilovici, C and Scantlebury, MH}, title = {Mechanisms of Infantile Epileptic Spasms Syndrome: What Have We Learnt From Animal Models?.}, journal = {Epilepsia}, volume = {}, number = {}, pages = {}, doi = {10.1111/epi.17841}, pmid = {38036453}, issn = {1528-1167}, abstract = {The devastating developmental and epileptic encephalopathy of infantile epileptic spasms syndrome (IESS) has numerous causes, including, but not limited to, brain injury, metabolic, and genetic conditions. Given the stereotyped electrophysiologic, age-dependent, and clinical findings, there likely exists one or more final common pathway in the development of IESS. The identity of this final common pathway is unknown, but it may represent a novel therapeutic target for infantile spasms. Previous research on IESS has largely focused on identifying the neuroanatomical substrate using specialized neuroimaging techniques and cerebrospinal fluid analysis in human patients. Over the past three decades, several animal models of IESS were created with an aim to interrogate the underlying pathogenesis of IESS, to identify novel therapeutic targets, and to test various treatments. Each of these models have been successful at recapitulating multiple aspects of the human IESS condition. These animal models have implicated several different molecular pathways in the development of infantile spasms. In this review we outline the progress that has been made thus far using these animal models and discuss future directions to help researchers identify novel treatments for drug-resistant IESS.}, }
@article {pmid38036425, year = {2023}, author = {Doolin, ML and Dearing, MD}, title = {Differential effects of two common antiparasitics on microbiota resilience.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiad547}, pmid = {38036425}, issn = {1537-6613}, abstract = {BACKGROUND: Parasitic infections challenge vertebrate health worldwide, and off-target effects of antiparasitic treatments may be an additional obstacle to recovery. However, there have been few investigations of the effects of antiparasitics on the gut microbiome in the absence of parasites.<br><br>METHODS: We investigated whether two common antiparasitics-albendazole and metronidazole-significantly alter the gut microbiome of parasite-free mice. We treated mice with albendazole or metronidazole daily for seven days and sampled the fecal microbiota immediately before and after treatment, and again after a two-week recovery period.<br><br>RESULTS: Albendazole did not immediately change the gut microbiota, while metronidazole decreased microbial richness by 8.5% and significantly changed community structure during treatment. The structural changes caused by metronidazole included depletion of the beneficial family Lachnospiraceae, and predictive metagenomic analysis revealed that these losses likely depressed microbiome metabolic function. Separately, we compared the fecal microbiotas of treatment groups after recovery, and there were minor differences in community structure between the albendazole, metronidazole, and sham-treated control groups.<br><br>CONCLUSIONS: These results suggest that a healthy microbiome is resilient after metronidazole-induced depletions of beneficial gut microbes and albendazole may cause slight, latent shifts in the microbiota but does not deplete healthy gut microbiota diversity.}, }
@article {pmid38036127, year = {2023}, author = {Zhao, J and Yu, X and Zhang, C and Hou, L and Wu, N and Zhang, W and Wang, Y and Yao, B and Delaplace, P and Tian, J}, title = {Harnessing microbial interactions with rice: Strategies for abiotic stress alleviation in the face of environmental challenges and climate change.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {168847}, doi = {10.1016/j.scitotenv.2023.168847}, pmid = {38036127}, issn = {1879-1026}, abstract = {Rice, which feeds more than half of the world's population, confronts significant challenges due to environmental and climatic changes. Abiotic stressors such as extreme temperatures, drought, heavy metals, organic pollutants, and salinity disrupt its cellular balance, impair photosynthetic efficiency, and degrade grain quality. Beneficial microorganisms from rice and soil microbiomes have emerged as crucial in enhancing rice's tolerance to these stresses. This review delves into the multifaceted impacts of these abiotic stressors on rice growth, exploring the origins of the interacting microorganisms and the intricate dynamics between rice-associated and soil microbiomes. We highlight their synergistic roles in mitigating rice's abiotic stresses and outline rice's strategies for recruiting these microorganisms under various environmental conditions, including the development of techniques to maximize their benefits. Through an in-depth analysis, we shed light on the multifarious mechanisms through which microorganisms fortify rice resilience, such as modulation of antioxidant enzymes, enhanced nutrient uptake, plant hormone adjustments, exopolysaccharide secretion, and strategic gene expression regulation, emphasizing the objective of leveraging microorganisms to boost rice's stress tolerance. The review also recognizes the growing prominence of microbial inoculants in modern rice cultivation for their eco-friendliness and sustainability. We discuss ongoing efforts to optimize these inoculants, providing insights into the rigorous processes involved in their formulation and strategic deployment. In conclusion, this review emphasizes the importance of microbial interventions in bolstering rice agriculture and ensuring its resilience in the face of rising environmental challenges.}, }
@article {pmid38036110, year = {2023}, author = {Kulshrestha, M and Tiwari, M and Tiwari, V}, title = {Bacteriophage therapy against ESKAPE bacterial pathogens: Current status, strategies, challenges, and future scope.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {106467}, doi = {10.1016/j.micpath.2023.106467}, pmid = {38036110}, issn = {1096-1208}, abstract = {The ESKAPE pathogens are the primary threat due to their constant spread of drug resistance worldwide. These pathogens are also regarded as opportunistic pathogens and could potentially cause nosocomial infections. Most of the ESKAPE pathogens have developed resistance to almost all the antibiotics that are used against them. Therefore, to deal with antimicrobial resistance, there is an urgent requirement for alternative non-antibiotic strategies to combat this rising issue of drug-resistant organisms. One of the promissing alternatives to this scenario is implementing bacteriophage therapy. This under-explored mode of treatment in modern medicine has posed several concerns, such as preferable phages for the treatment, impact on the microbiome (or gut microflora), dose optimisation, safety, etc. The review will cover a rationale for phage therapy, clinical challenges, and propose phage therapy as an effective therapeutic against bacterial coinfections during pandemics. This review also addresses the expected uncertainties for administering the phage as a treatment against the ESKAPE pathogens and the advantages of using lytic phage over temperate, the immune response to phages, and phages in combinational therapies. The interaction between bacteria and bacteriophages in humans and countless animal models can also be used to design novel and futuristic therapeutics like personalised medicine or bacteriophages as anti-biofilm agents. Hence, this review explores different aspects of phage therapy and its potential to emerge as a frontline therapy against ESKAPE bacterial pathogen.}, }
@article {pmid38035997, year = {2023}, author = {Chooi, YC and Zhang, QA and Magkos, F and Ng, M and Michael, N and Wu, X and Volchanskaya, VSB and Lai, X and Wanjaya, ER and Elejalde, U and Goh, CC and Yap, CPL and Wong, LH and Lim, KJ and Velan, SS and Yaligar, J and Muthiah, MD and Chong, YS and Loo, EXL and Eriksson, JG and ,  and Lim, KLM and Kouk, MSF and Mei Chong, EW and Gani, MA and Li, L and Tay, VHK and Kway, YM and Kumar, M and Sadananthan, SA and Khoo, K and Koh, D and Lim, R and Kang, CW and Sin, KL and Lim, JW}, title = {Effect of an Asian-adapted Mediterranean diet and pentadecanoic acid on fatty liver disease: The TANGO randomized controlled trial.}, journal = {The American journal of clinical nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajcnut.2023.11.013}, pmid = {38035997}, issn = {1938-3207}, abstract = {BACKGROUND: Weight loss is the most effective treatment for non-alcoholic fatty liver disease (NAFLD). There is evidence that Mediterranean diets rich in unsaturated fatty acids and fiber have beneficial effects on weight homeostasis and metabolic risk factors in individuals with NAFLD. Studies have also shown that higher circulating concentrations of pentadecanoic acid (C15:0) are associated with lower risk for NAFLD.<br><br>OBJECTIVES: To examine the effects of a Mediterranean-like, culturally contextualized Asian diet rich in fiber and unsaturated fatty acids, with or without C15:0 supplementation, in Chinese females with NAFLD.<br><br>METHODS: In a double-blinded, parallel-design, randomized controlled trial, 88 Chinese females with NAFLD were randomized to one of three groups for 12-weeks: diet with C15:0 supplementation (n=31), diet without C15:0 supplementation (n=28), or control (habitual diet and no C15:0 supplementation, n=29). At baseline and after the intervention, body fat percentage, intrahepatic lipid content, muscle and abdominal fat, liver enzymes, cardiometabolic risk factors and gut microbiome were assessed.<br><br>RESULTS: In intention-to-treat analysis, weight reductions of 4.0&#xb1;0.5 kg (5.3%), 3.4&#xb1;0.5 kg (4.5%), and 1.5&#xb1;0.5 kg (2.1%) were achieved in the diet-with-C15:0, diet-without-C15:0, and the control groups, respectively. The proton density fat fraction (PDFF) of the liver decreased by 33%, 30% and 10%, respectively. Both diet groups achieved significantly greater reductions in body weight, liver PDFF, total cholesterol, gamma-glutamyl transferase, and triglyceride concentrations compared to the control group. C15:0 supplementation reduced LDL-cholesterol further, and increased abundance of Bifidobacterium adolescentis. Fat mass, visceral adipose tissue, subcutaneous abdominal adipose tissue (deep and superficial), insulin, glycated hemoglobin and blood pressure decreased significantly in all groups, in parallel with weight loss.<br><br>CONCLUSION: Mild weight loss induced by a Mediterranean-like diet adapted for Asians has multiple beneficial health effects in women with NAFLD. C15:0 supplementation lowers LDL-cholesterol and may cause beneficial shifts in gut microbiome.<br><br>REGISTRATION: clinicaltrials.gov, NCT05259475.}, }
@article {pmid38035991, year = {2023}, author = {Balasubramanian, S and Haneen, MA and Sharma, G and Perumal, E}, title = {Acute copper oxide nanoparticles exposure alters zebrafish larval microbiome.}, journal = {Life sciences}, volume = {}, number = {}, pages = {122313}, doi = {10.1016/j.lfs.2023.122313}, pmid = {38035991}, issn = {1879-0631}, abstract = {Copper oxide nanoparticles (CuO NPs) are being used in healthcare industries due to its antimicrobial properties. The increased consumption of NPs could lead to the rise of these NPs in the environment affecting the biological systems. Altered microbiome has been correlated to disease pathology in humans as well as xenobiotic toxicity in experimental animal models. However, CuO NPs-induced microbiome alterations in vertebrates have not been reported so far. In this study for the first time, zebrafish larvae at 96 hpf (hours post fertilization) were exposed to CuO NPs for 24 h at 10, 20, and 40 ppm. After exposure, the control and treated larvae were subjected to 16S rRNA amplicon sequencing followed by relative taxa abundance, alpha and beta diversity analysis, single factor analysis, LEfSe, Deseq2, and functional profiling. No significant alteration was detected in the microbial richness and diversity, however, specific taxa constituting the core microbiome such as the phylum Proteobacteria were significantly increased and Bacterioidetes and Firmicutes were decreased in the treated groups, indicating a core microbiota dysbiosis. Further, the family Lachnospiraceae, and genus Syntrophomonas involved in butyrate production and the metabolism of lipids and glucose were significantly altered. In addition, the opportunistic pathogens belonging to order Flavobacteriales were increased in CuO NPs treated groups. Moreover, the taxa involved in host immune response (Shewanella, Delftia, and Bosea) were found to be enriched in CuO NPs exposed larvae. These results indicate that CuO NPs exposure causes alteration in the core microbiota, which could cause colitis or inflammatory bowel disease.}, }
@article {pmid38035748, year = {2023}, author = {Reynolds, AN and Hood, F and Wilson, R and Ross, A and Neumann, S and Turner, R and Iosua, E and Katare, R and Shahin, A and Kok, ZY and Chan, H and Coffey, S and Mann, J}, title = {Healthy grocery delivery in the usual care for adults recovering from an acute coronary event: protocol for a three-arm randomised controlled trial.}, journal = {BMJ open}, volume = {13}, number = {11}, pages = {e074278}, pmid = {38035748}, issn = {2044-6055}, abstract = {INTRODUCTION: Coronary heart disease is a major contributor to the global burden of disease. Appropriate nutrition is a cornerstone of the prevention and treatment of coronary heart disease; however, barriers including cost and access to recommended foods limits long-term adherence for many. We are conducting, in adults with coronary heart disease, a randomised controlled trial comparing usual care with two dietary interventions in which usual care is augmented by 12 weeks free delivered groceries.<br><br>METHODS AND ANALYSIS: Three hundred adults recovering from an acute coronary event will be recruited from outpatient cardiovascular services in three regions of Aotearoa New Zealand. Participants will be randomly allocated to three arms: usual care (control group), usual care and the free delivery of foods high in dietary fibre or usual care and the free delivery of foods high in unsaturated fats. Interventions duration is 12 weeks, with a further 12 months follow-up. The primary outcome measures are change in low-density lipoprotein (LDL) cholesterol concentration following the intervention, and a cost-effectiveness analysis of healthcare access and social costs in the year after the intervention. A broad range of secondary outcome measures include other blood lipids, anthropometry, glycaemia, inflammatory markers, gut microbiome, dietary biomarkers, food acceptability, dietary change and the facilitators and barriers to dietary change. The trial will determine whether the free provision of groceries known to reduce cardiovascular risk within usual care will be clinically beneficial and justify the cost of doing so. Results may also provide an indication of the relative benefit of foods rich in dietary fibre or unsaturated fats in coronary heart disease management.<br><br>ETHICS AND DISSEMINATION: This trial, The Healthy Heart Study, has Health and Disability Ethics Committee approval (20/NTB/121), underwent M&#x101;ori consultation, and has locality authority to be conducted in Canterbury, Otago and Southland.<br><br>TRIAL REGISTRATION NUMBER: ACTRN12620000689976, U1111-1250-1499.}, }
@article {pmid38035726, year = {2023}, author = {Zhou, H and Wang, L and Lin, Z and Jiang, C and Chen, X and Wang, K and Liu, L and Shao, L and Pan, J and Li, J and Zhang, D and Wu, J}, title = {Methylglyoxal from gut microbes boosts radiosensitivity and radioimmunotherapy in rectal cancer by triggering endoplasmic reticulum stress and cGAS-STING activation.}, journal = {Journal for immunotherapy of cancer}, volume = {11}, number = {11}, pages = {}, pmid = {38035726}, issn = {2051-1426}, abstract = {BACKGROUND: Preoperative radiation therapy (preRT) is a fundamental aspect of neoadjuvant treatment for rectal cancer (RC), but the response to this treatment remains unsatisfactory. The combination of radiation therapy (RT) and immunotherapy (iRT) presents a promising approach to cancer treatment, though the underlying mechanisms are not yet fully understood. The gut microbiota may influence the response to RT and immunotherapy. Therefore, we aimed to identify the metabolism of gut microbiota to reverse radioresistance and enhance the efficacy of iRT.<br><br>METHODS: Fecal and serum samples were prospectively collected from patients with locally advanced rectal cancer (LARC) who had undergone pre-RT treatment. Candidate gut microbiome-derived metabolites linked with radiosensitization were screened using 16s rRNA gene sequencing and ultrahigh-performance liquid chromatography-mass coupled with mass spectrometry. In vitro and in vivo studies were conducted to assess the radiosensitizing effects of the metabolites including the syngeneic CT26 tumor model and HCT116 xenograft tumor model, transcriptomics and immunofluorescence. The CT26 abscopal effect modeling was employed to evaluate the combined effects of metabolites on iRT.<br><br>RESULTS: We initially discovered the gut microbiota-associated metabolite, methylglyoxal (MG), which accurately predicts the response to preRT (Area Under Curve (AUC) value of 0.856) among patients with LARC. Subsequently, we observed that MG amplifies the RT response in RC by stimulating intracellular reactive oxygen species (ROS) and reducing hypoxia in the tumor in vitro and in vivo. Additionally, our study demonstrated that MG amplifies the RT-induced activation of the cyclic guanosine monophosphate AMP synthase-stimulator of interferon genes pathway by elevating DNA double-strand breaks. Moreover, it facilitates immunogenic cell death generated by ROS-mediated endoplasmic reticulum stress, consequently leading to an increase in CD8[+] T and natural killer cells infiltrated in the tumor immune microenvironment. Lastly, we discovered that the combination of anti-programmed cell death protein 1 (anti-PD1) therapy produced long-lasting complete responses in all irradiated tumor sites and half of the non-irradiated ones.<br><br>CONCLUSIONS: Our research indicates that MG shows promise as a radiosensitizer and immunomodulator for RC. Furthermore, we propose that combining MG with iRT has great potential for clinical practice.}, }
@article {pmid38035660, year = {2023}, author = {Luise, D and Correa, F and Negrini, C and Virdis, S and Mazzoni, M and Dalcanale, S and Trevisi, P}, title = {Blend of natural and natural identical essential oil compounds as a strategy to improve the gut health of weaning pigs.}, journal = {Animal : an international journal of animal bioscience}, volume = {17}, number = {12}, pages = {101031}, doi = {10.1016/j.animal.2023.101031}, pmid = {38035660}, issn = {1751-732X}, abstract = {Weaning is one of the most critical phases in pig's life, often leading to postweaning diarrhoea (PWD). Zinc oxide (ZnO), at pharmacological doses, has been largely used to prevent PWD; however, due to antimicrobial co-resistant and environmental pollution issues, the EU banned its use in June 2022. Natural or natural identical components of essential oils and their mixture with organic acids are possible alternatives studied for their antimicrobial, anti-inflammatory and antioxidant abilities. This study aimed to evaluate the effect of two blends of natural or natural identical components of essential oils and organic acids compared to ZnO on health, performance, and gut health of weaned pigs. At weaning (d0), 96 piglets (7 058 ± 895 g) were assigned to one of four treatments balanced for BW and litter: CO (control treatment), ZnO (2 400 mg/kg ZnO from d0 to d14); Blend1 (cinnamaldehyde, ajowan and clove essential oils, 1 500 mg/kg feed); Blend2 (cinnamaldehyde, eugenol and short- and medium-chain fatty acids, 2 000 mg/kg feed). Pigs were weighed weekly until d35. Faeces were collected at d13 and d35 for microbiota (v3-v4 regions of the 16 s rRNA gene) and Escherichia coli (E. coli) count analysis. At d14 and d35, eight pigs/treatment were slaughtered; pH was recorded on intestinal contents and jejunal samples were collected for morphological and gene expression analysis. From d7-d14, the Blend2 had a lower average daily gain (ADG) than CO and ZnO (P < 0.05). ZnO and Blend1 never differed in ADG and feed intake. At d14, ZnO had a lower caecum pH than all other treatments. The CO treatment had a higher abundance of haemolytic E. coli than Blend1 (P = 0.01). At d13, the ZnO treatment had a lower alpha diversity (P < 0.01) and a different microbial beta diversity (P < 0.001) compared to the other treatments. At d13, the ZnO treatment was characterised by a higher abundance of Prevotellaceae_NK3B31_group (Linear Discriminant Analysis (LDA) score = 4.5, P = 0.011), Parabacteroides (LDA score = 4.5, P adj. = 0.005), the CO was characterised by Oscillospiraceae UCG-005 (LDA score = 4.3, P adj. = 0.005), Oscillospiraceae NK4A214_group (LDA score = 4.2, P adj. = 0.02), the Blend2 was characterised by Megasphaera (LDA score = 4.1, P adj. = 0.045), and Ruminococcus (LDA score = 3.9, P adj. = 0.015) and the Blend1 was characterised by Christensenellaceae_R-7_group (LDA score = 4.6, P adj. < 0.001) and Treponema (LDA score = 4.5, P adj. < 0.001). In conclusion, Blend1 allowed to maintain the gut health of postweaning piglets through modulation of the gut microbiome, the reduction of haemolytic E. coli while Blend2 did not help piglets.}, }
@article {pmid38035522, year = {2023}, author = {Nguyen, AH and Oh, S}, title = {Side effects of the addition of an adsorbent for the nitrification performance of a microbiome in the treatment of an antibiotic mixture.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133034}, doi = {10.1016/j.jhazmat.2023.133034}, pmid = {38035522}, issn = {1873-3336}, abstract = {This work determined the effect of biochar (BC) as an adsorbent on the nitrifying microbiome in regulating the removal, transformation, fate, toxicity, and potential environmental consequences of an antibiotic mixture containing oxytetracycline (OTC) and sulfamethoxazole (SMX). Despite the beneficial role of BC as reported in the literature, the present study revealed side effects for the nitrifying microbiome and its functioning arising from the presence of BC. Long-term monitoring revealed severe disruption to nitratation via the inhibition of both nitrite oxidizers (e.g., Nitrospira defluvii) and potential comammox species (e.g., Ca. Nitrospira nitrificans). Byproducts (BPs) more toxic than the parent compounds were found to persist at a high relative abundance, particularly in the presence of BC. Quantitative structure-activity relationship modeling determined that the physicochemical properties of the toxic BPs significantly differed from those of OTC and SMX. The results suggested that the BPs tended to mobilize and accumulate on the surface of the solids in the system (i.e., the BC and biofilm), disrupting the nitrifiers growing at the interface. Collectively, this study provides novel insights, demonstrating that the addition of adsorbents to biological systems may not necessarily be beneficial; rather, they may generate side effects for specific bacteria that have important ecosystem functions.}, }
@article {pmid38035404, year = {2023}, author = {Lindner, BG and Gerhardt, K and Feistel, DJ and Rodriguez-R, LM and Hatt, JK and Konstantinidis, KT}, title = {A user's guide to the bioinformatic analysis of shotgun metagenomic sequence data for bacterial pathogen detection.}, journal = {International journal of food microbiology}, volume = {410}, number = {}, pages = {110488}, doi = {10.1016/j.ijfoodmicro.2023.110488}, pmid = {38035404}, issn = {1879-3460}, abstract = {Metagenomics, i.e., shotgun sequencing of the total microbial community DNA from a sample, has become a mature technique but its application to pathogen detection in clinical, environmental, and food samples is far from common or standardized. In this review, we summarize ongoing developments in metagenomic sequence analysis that facilitate its wider application to pathogen detection. We examine theoretical frameworks for estimating the limit of detection for a particular level of sequencing effort, current approaches for achieving species and strain analytical resolution, and discuss some relevant modern tools for these tasks. While these recent advances are significant and establish metagenomics as a powerful tool to provide insights not easily attained by culture-based approaches, metagenomics is unlikely to emerge as a widespread, routine monitoring tool in the near future due to its inherently high detection limits, cost, and inability to easily distinguish between viable and non-viable cells. Instead, metagenomics seems best poised for applications involving special circumstances otherwise challenging for culture-based and molecular (e.g., PCR-based) approaches such as the de novo detection of novel pathogens, cases of co-infection by more than one pathogen, and situations where it is important to assess the genomic composition of the pathogenic population(s) and/or its impact on the indigenous microbiome.}, }
@article {pmid38035339, year = {2023}, author = {Li, K and Deng, J and Zhang, C and Lai, G and Xie, B and Zhong, X}, title = {Gut microbiome dysbiosis in men who have sex with men increases HIV infection risk through immunity homeostasis alteration.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1260068}, pmid = {38035339}, issn = {2235-2988}, abstract = {OBJECTIVES: Recent studies pointed out that gut microbiome dysbiosis in HIV infection was possibly confounded in men who have sex with men (MSM), but there is a lack of evidence. It also remained unclear how MSM-associated gut microbiome dysbiosis affected human health. This study aimed to compare the differences in gut microbiome changes between HIV and MSM and reveal the potential impacts of MSM-associated gut microbiome dysbiosis on the immune system.<br><br>METHODS: We searched available studies based on the PubMed database, and all gut microbiome changes associated with HIV infection and MSM were extracted from the enrolled studies. The gutMgene database was used to identify the target genes and metabolites of the gut microbiome. Bioinformatic technology and single-cell RNA sequencing data analysis were utilized to explore the impacts of these gut microbiome changes on human immunity.<br><br>RESULTS: The results showed significant overlaps between the gut microbiome associated with HIV and that of MSM. Moreover, bioinformatic analysis revealed that gut microbiome dysbiosis in MSM had an impact on several pathways related to immunity, including the IL-17 signaling pathway and Th17 cell differentiation. Additionally, target genes of MSM-associated gut microbiome were found to be highly expressed in monocytes and lymphocytes, suggesting their potential regulatory role in immune cells. Furthermore, we found that MSM-associated gut microbiome could produce acetate and butyrate which were reported to increase the level of inflammatory factors.<br><br>CONCLUSION: In conclusion, this study highlighted that MSM-associated gut microbiome dysbiosis might increase the risk of HIV acquisition by activating the immune system. Further studies are expected to elucidate the mechanism by which gut microbiome dysbiosis in MSM modulates HIV susceptibility.}, }
@article {pmid38035338, year = {2023}, author = {Van Dingenen, L and Segers, C and Wouters, S and Mysara, M and Leys, N and Kumar-Singh, S and Malhotra-Kumar, S and Van Houdt, R}, title = {Dissecting the role of the gut microbiome and fecal microbiota transplantation in radio- and immunotherapy treatment of colorectal cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1298264}, pmid = {38035338}, issn = {2235-2988}, abstract = {Colorectal cancer (CRC) is one of the most commonly diagnosed cancers and poses a major burden on the human health worldwide. At the moment, treatment of CRC consists of surgery in combination with (neo)adjuvant chemotherapy and/or radiotherapy. More recently, immune checkpoint blockers (ICBs) have also been approved for CRC treatment. In addition, recent studies have shown that radiotherapy and ICBs act synergistically, with radiotherapy stimulating the immune system that is activated by ICBs. However, both treatments are also associated with severe toxicity and efficacy issues, which can lead to temporary or permanent discontinuation of these treatment programs. There's growing evidence pointing to the gut microbiome playing a role in these issues. Some microorganisms seem to contribute to radiotherapy-associated toxicity and hinder ICB efficacy, while others seem to reduce radiotherapy-associated toxicity or enhance ICB efficacy. Consequently, fecal microbiota transplantation (FMT) has been applied to reduce radio- and immunotherapy-related toxicity and enhance their efficacies. Here, we have reviewed the currently available preclinical and clinical data in CRC treatment, with a focus on how the gut microbiome influences radio- and immunotherapy toxicity and efficacy and if these treatments could benefit from FMT.}, }
@article {pmid38035128, year = {2024}, author = {Martinez, R and Mayur, O and Pagani, K and Lukac, D and McGee, JS}, title = {Topical tretinoin alters skin microbiota in patients with mild acne.}, journal = {JAAD international}, volume = {14}, number = {}, pages = {1-3}, pmid = {38035128}, issn = {2666-3287}, }
@article {pmid38035090, year = {2023}, author = {Gu, J and Zhang, J and Liu, Q and Xu, S}, title = {Neurological risks of COVID-19 in women: the complex immunology underpinning sex differences.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1281310}, pmid = {38035090}, issn = {1664-3224}, abstract = {The COVID-19 pandemic has uncovered many mysteries about SARS-CoV-2, including its potential to trigger abnormal autoimmune responses. Emerging evidence suggests women may face higher risks from COVID-induced autoimmunity manifesting as persistent neurological symptoms. Elucidating the mechanisms underlying this female susceptibility is now imperative. We synthesize key insights from existing studies on how COVID-19 infection can lead to immune tolerance loss, enabling autoreactive antibodies and lymphocyte production. These antibodies and lymphocytes infiltrate the central nervous system. Female sex hormones like estrogen and X-chromosome mediated effects likely contribute to dysregulated humoral immunity and cytokine profiles among women, increasing their predisposition. COVID-19 may also disrupt the delicate immunological balance of the female microbiome. These perturbations precipitate damage to neural damage through mechanisms like demyelination, neuroinflammation, and neurodegeneration - consistent with the observed neurological sequelae in women. An intentional focus on elucidating sex differences in COVID-19 pathogenesis is now needed to inform prognosis assessments and tailored interventions for female patients. From clinical monitoring to evaluating emerging immunomodulatory therapies, a nuanced women-centered approach considering the hormonal status and immunobiology will be vital to ensure equitable outcomes. Overall, deeper insights into the apparent female specificity of COVID-induced autoimmunity will accelerate the development of solutions mitigating associated neurological harm.}, }
@article {pmid38035082, year = {2023}, author = {Deng, WY and Chen, WJ and Zhong, HJ and Wu, LH and He, XX}, title = {Washed microbiota transplantation: a case report of clinical success with skin and gut microbiota improvement in an adolescent boy with atopic dermatitis.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1275427}, pmid = {38035082}, issn = {1664-3224}, abstract = {Atopic dermatitis (AD) is a chronic, recurrent inflammatory disease characterized by itching. The gut microbiome can help maintain skin immune homeostasis by regulating innate and adaptive immunity. Here, we report a case of AD in a 15-year-old adolescent boy who benefited from washed microbiota transplantation (WMT). WMT was performed for three courses, with each course lasting for three consecutive days and an interval of one month between two courses. Clinical assessments were conducted at each WMT course, and skin, blood, and stool samples were collected for microbial analysis. After three months of WMT treatment, the boy's itchiness was effectively controlled: his skin showed noticeable improvement, with reduced Staphylococcus aureus in the skin lesions. The scores of SCORAD (SCORing Atopic Dermatitis), EASI (Eczema Area and Severity Index), NRS (Numerical Rating Scale), and DLQI (Dermatology Life Quality Index) significantly decreased compared to the baseline. Serum levels of eosinophil ratio, tumor necrotic factor-α, and interleukin-6 also reduced to the normal levels. There was a significant decrease in S. aureus in the skin lesions. Additionally, the intestinal flora became more diverse, and the abundance of Bifidobacterium species, significantly increased after WMT. No adverse events were reported during the treatment and the 1-year follow-up period. This case report provides direct clinical evidence for WMT as a novel promising treatment strategy for AD, and preliminary experimental data suggests the existence of an intestinal-skin axis in terms of the gut microbiota and the skin immune homeostasis.}, }
@article {pmid38034829, year = {2023}, author = {Monleón-Getino, A and Pujol-Muncunill, G and Méndez Viera, J and Álvarez Carnero, L and Sanseverino, W and Paytuví-Gallart, A and Martín de Carpí, J}, title = {A pilot study of the use of the oral and faecal microbiota for the diagnosis of ulcerative colitis and Crohn's disease in a paediatric population.}, journal = {Frontiers in pediatrics}, volume = {11}, number = {}, pages = {1220976}, pmid = {38034829}, issn = {2296-2360}, abstract = {Crohn's disease (CD) and ulcerative colitis (UC) are chronic inflammatory bowel diseases (IBD) that affect the gastrointestinal tract. Changes in the microbiome and its interaction with the immune system are thought to play a key role in their development. The aim of this study was to determine whether metagenomic analysis is a feasible non-invasive diagnostic tool for IBD in paediatric patients. A pilot study of oral and faecal microbiota was proposed with 36 paediatric patients divided in three cohorts [12 with CD, 12 with UC and 12 healthy controls (HC)] with 6 months of follow-up. Finally, 30 participants were included: 13 with CD, 11 with UC and 8 HC (6 dropped out during follow-up). Despite the small size of the study population, a differential pattern of microbial biodiversity was observed between IBD patients and the control group. Twenty-one bacterial species were selected in function of their discriminant accuracy, forming three sets of potential markers of IBD. Although IBD diagnosis requires comprehensive medical evaluation, the findings of this study show that faecal metagenomics or a reduced set of bacterial markers could be useful as a non-invasive tool for an easier and earlier diagnosis.}, }
@article {pmid38034672, year = {2023}, author = {Oyeyemi, BF and Kaur, US and Paramraj, A and Chintamani,  and Tandon, R and Kumar, A and Bhavesh, NS}, title = {Microbiome analysis of saliva from oral squamous cell carcinoma (OSCC) patients and tobacco abusers with potential biomarkers for oral cancer screening.}, journal = {Heliyon}, volume = {9}, number = {11}, pages = {e21773}, pmid = {38034672}, issn = {2405-8440}, abstract = {Oral squamous cell carcinoma (OSCC) is the most common type of oral cancer and accounts for about 95% of all head and neck cancers with high mortality, usually at a late stage. Dysbiosis in the oral microbiome can lead to chronic inflammatory responses and may predispose to the development and progression of OSCC. Tobacco abuse plays an essential role in oral microbiome dysregulation and OSCC pathogenesis. We used 16S rRNA gene amplicon next-generation sequencing to examine microbial signatures unique to saliva from OSCC patients, tobacco abusers (TA) and controls (n = 10 for each group) to elucidate oral microbiome changes associated with tobacco abuse and OSCC. Overall, the oral microbiome compositions of class Betaproteobacteria and Epsilonproteobacteria, order Neisseriales, Burkholderiales and Campylobacterales, family Burkholderiaceae and Campylobacteraceae and genera Campylobacter and Leptotrichia revealed significant differences among OSCC patients, TA and control. Our preliminary pilot study not only serves as a basis for future studies with large sample size but also gives an indication of microbiome-based potential non-invasive biomarkers for early screening and monitoring of oral carcinogenesis transition due to tobacco abuse.}, }
@article {pmid38034657, year = {2023}, author = {Fu, J and Liang, Y and Shi, Y and Yu, D and Wang, Y and Chen, P and Liu, S and Lu, F}, title = {HuangQi ChiFeng decoction maintains gut microbiota and bile acid homeostasis through FXR signaling to improve atherosclerosis.}, journal = {Heliyon}, volume = {9}, number = {11}, pages = {e21935}, pmid = {38034657}, issn = {2405-8440}, abstract = {Huangqi Chifeng Decoction (HQCFT), a traditional Chinese medicine preparation, has long been used to treat cardiovascular and cerebrovascular diseases. However, the mechanism of the beneficial effect of HQCFT on atherosclerosis remains to be explored. In this work, to investigate the effects of HQCFT on bile acid (BA) metabolism and the gut microbiome in atherosclerosis, ApoE[-/-] mice were fed a with high-fat diet for 16 weeks to establish the AS model. HQCFT(1.95 g kg[-1] and 3.9 g kg[-1] per day) was administered intragastrically for 8 weeks to investigate the regulatory effects of HQCFT on gut microbiota and bile acid metabolism and to inhibit the occurrence and development of AS induced by a high-fat diet. Histopathology, liver function and blood lipids were used to assess whether HQCFT can reduce plaque area, regulate lipid levels and alleviate liver steatosis in AS mice. In addition, 16S rDNA sequencing was used to screen the gut microbiota structure, and ultrahigh-performance liquid chromatography-tandem mass spectrometry (UPLC‒MS/MS) was used to determine the bile acid profile. The mRNA and protein expression levels of bile acid metabolism were detected by RT‒PCR and WB to find the potential correlation. Results: HQCFT can regulate gut microbiota disorders, which was achieved by increasing gut microbiota diversity and altering Proteobacteria, Desulfobacterota, Deferribacteres, Rodentibacter, Parasutterella, and Mucispirillum interference abundance to improve AS-induced gut microbiota. HQCFT can also adjust the content of bile acids (TCA, LCA, DCA, TDCA, TLCA, UDCA, etc.), regulate bile acid metabolism, relieve liver fat accumulation, and inhibit the process of AS. In addition, HQCFT can restore the abnormal metabolism of bile acid caused by AS by regulating the expression of farnesoid X receptor (FXR), liver X receptor α (LXRα), ABCA1, ABCG1 and CYP7A1. Conclusion: HQCFT may play a part in the prevention of atherosclerosis by inhibiting the FXR/LXRα axis, increasing the expression of CYP7A1 in the liver, and regulating the interaction between the gut microbiota and bile acid metabolism.}, }
@article {pmid38034621, year = {2023}, author = {Jiang, W and Lu, G and Qiao, T and Yu, X and Luo, Q and Tong, J and Fan, S and Chai, L and Gao, D and Wang, R and Deng, C and Lv, Z and Li, D}, title = {Integrated microbiome and metabolome analysis reveals a distinct microbial and metabolic signature in Graves' disease and hypothyroidism.}, journal = {Heliyon}, volume = {9}, number = {11}, pages = {e21463}, pmid = {38034621}, issn = {2405-8440}, abstract = {Recent studies reveal that imbalanced microbiota is related to thyroid diseases. However, studies on the alterations in fecal metabolites in Graves' disease and clinical hypothyroidism patients are insufficient. Here, we identified 21 genera and 53 metabolites that were statistically significant among Graves' disease patients, hypothyroidism patients, and controls integrating microbiome and untargeted metabolome analysis. Disease groups revealed a decreased abundance in butyrate-producing microbiota and an increased abundance in potentially pathogenic microbiota. Lipids molecules were the major differential metabolites identified in all fecal samples. Network analysis recognized that microbiota may affect thyroid function by targeting specific metabolites. We further identified specific microbiota and metabolites that could distinguish Graves' disease patients, hypothyroidism patients, and controls. Our study reveals a distinct microbial and metabolic signature in hypothyroidism patients and Graves' disease patients and further validates the potential role of microbiota in thyroid diseases, providing new ideas for future research into the etiology and clinical intervention of thyroid diseases.}, }
@article {pmid38034569, year = {2023}, author = {Xia, K and Feng, Z and Zhang, X and Zhou, Y and Zhu, H and Yao, Q}, title = {Potential functions of the shared bacterial taxa in the citrus leaf midribs determine the symptoms of Huanglongbing.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1270929}, pmid = {38034569}, issn = {1664-462X}, abstract = {INSTRUCTION: Citrus is a globally important fruit tree whose microbiome plays a vital role in its growth, adaptability, and resistance to stress.<br><br>METHODS: With the high throughput sequencing of 16S rRNA genes, this study focused on analyzing the bacterial community, especially in the leaf midribs, of healthy and Huanglongbing (HLB)-infected plants.<br><br>RESULTS: We firstly identified the shared bacterial taxa in the midribs of both healthy and HLB-infected plants, and then analyzed their functions. Results showed that the shared bacterial taxa in midribs belonged to 62 genera, with approximately 1/3 of which modified in the infected samples. Furthermore, 366 metabolic pathways, 5851 proteins, and 1833 enzymes in the shared taxa were predicted. Among these, three metabolic pathways and one protein showed significant importance in HLB infection. With the random forest method, six genera were identified to be significantly important for HLB infection. Notably, four of these genera were also among the significantly different shared taxa. Further functional characterization of these four genera revealed that Pseudomonas and Erwinia likely contributed to plant defense against HLB, while Streptomyces might have implications for plant defense against HLB or the pathogenicity of Candidatus Liberibacter asiaticus (CLas).<br><br>DISCCUSION: Overall, our study highlights that the functions of the shared taxa in leaf midribs are distinguished between healthy and HLB-infected plants, and these microbiome-based findings can contribute to the management and protection of citrus crops against CLas.}, }
@article {pmid38034470, year = {2023}, author = {Mukhi, S and Dhanashree, B and Srikantiah, RM and Manjrekar, P and Harish, S}, title = {Evaluation of Minimum Inhibitory Concentration of Heavy Metals Contained in Packaging Material Digest on Prominent Gut Microbiota.}, journal = {International journal of food science}, volume = {2023}, number = {}, pages = {3840795}, pmid = {38034470}, issn = {2314-5765}, abstract = {Several scientific investigations have revealed that the leaching of metals from packaging material into the packed food is an unavoidable process. Hence, this study is aimed at investigating the effect of leached heavy metals from food packing materials on normal human gut flora. We analysed the effect of vanadium, arsenic, cadmium, and mercury present in digested packaging materials (DPM) on standard strains of Escherichia coli ATCC 25923, Pseudomonas aeruginosa ATCC 27853, Klebsiella pneumoniae ATCC 70063, and Enterococcus faecalis ATCC 29212. The minimum inhibitory concentration (MIC) of laboratory-grade heavy metal salts and heavy metals present in DPM was determined by the agar dilution method. For all four bacteria, the MIC of cadmium and arsenic in the DPM was 7 μg/ml and 1.6 μg/ml, respectively. The MIC of mercury in DPM was 1.6 μg/ml for E. coli, K. pneumoniae, and E. faecalis and 1.4 μg/ml for P. aeruginosa. MIC of vanadium for E. coli, P. aeruginosa, and E. faecalis was 2.2 μg/ml, and for K. pneumoniae was 2.0 μg/ml. The difference in MICs of heavy metals in DPMs and heavy metal salts was not statistically significant. MICs were within CODEX-specified permissible levels. Though heavy metals in packaging material have not shown a deleterious effect on representative human gut flora, there is scope to study their effect on the gut microbiome. Thus, understanding the risk of heavy metal ingestion through unknown sources and avoiding any possible ingestion is crucial to preventing chronic diseases.}, }
@article {pmid38034007, year = {2023}, author = {Abuqwider, J and Corrado, A and Scidà, G and Lupoli, R and Costabile, G and Mauriello, G and Bozzetto, L}, title = {Gut microbiome and blood glucose control in type 1 diabetes: a systematic review.}, journal = {Frontiers in endocrinology}, volume = {14}, number = {}, pages = {1265696}, pmid = {38034007}, issn = {1664-2392}, abstract = {OBJECTIVE: The risk of developing micro- and macrovascular complications is higher for individuals with type 1 diabetes (T1D). Numerous studies have indicated variations in gut microbial composition between healthy individuals and those with T1D. These changes in the gut ecosystem may lead to inflammation, modifications in intestinal permeability, and alterations in metabolites. Such effects can collectively impact the metabolic regulation system, thereby influencing blood glucose control. This review aims to explore the relationship between the gut microbiome, inflammation, and blood glucose parameters in patients with T1D.<br><br>METHODS: Google Scholar, PubMed, and Web of Science were systematically searched from 2003 to 2023 using the following keywords: "gut microbiota," "gut microbiome," "bacteria," "T1D," "type 1 diabetes," "autoimmune diabetes," "glycemic control," "glucose control," "HbA1c," "inflammation," "inflammatory," and "cytokine." The examination has shown 18,680 articles with relevant keywords. After the exclusion of irrelevant articles, seven observational papers showed a distinct gut microbial signature in T1D patients.<br><br>RESULTS: This review shows that, in T1D patients, HbA1c level was negatively correlated with abundance of Prevotella, Faecalibacterium, and Ruminococcaceae and positively correlated with abundance of Dorea formicigenerans, Bacteroidetes, Lactobacillales, and Bacteriodes. Instead, Bifidobacteria was negatively correlated with fasting blood glucose. In addition, there was a positive correlation between Clostridiaceae and time in range. Furthermore, a positive correlation between inflammatory parameters and gut dysbiosis was revealed in T1D patients.<br><br>CONCLUSION: We draw the conclusion that the gut microbiome profiles of T1D patients and healthy controls differ. Patients with T1D may experience leaky gut, bacterial translocation, inflammation, and poor glucose management due to microbiome dysbiosis. Direct manipulation of the gut microbiome in humans and its effects on gut permeability and glycemic control, however, have not been thoroughly investigated. Future research should therefore thoroughly examine other potential pathophysiological mechanisms in larger studies.}, }
@article {pmid38033919, year = {2023}, author = {Bautista-Becerril, B and Budden, KF and Falfán-Valencia, R}, title = {Editorial: Microbiota and asthma.}, journal = {Frontiers in allergy}, volume = {4}, number = {}, pages = {1297425}, pmid = {38033919}, issn = {2673-6101}, }
@article {pmid38033643, year = {2023}, author = {Centeno-Martinez, RE and Klopp, RN and Koziol, J and Boerman, JP and Johnson, TA}, title = {Dynamics of the nasopharyngeal microbiome of apparently healthy calves and those with clinical symptoms of bovine respiratory disease from disease diagnosis to recovery.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1297158}, pmid = {38033643}, issn = {2297-1769}, abstract = {INTRODUCTION: Bovine respiratory disease (BRD) is a multifactorial disease complex in which bacteria in the upper respiratory tract play an important role in disease development. Previous studies have related the presence of four BRD-pathobionts (Mycoplasma bovis, Histophilus somni, Pasteurella multocida, and Mannheimia haemolytica) in the upper respiratory tract to BRD incidence and mortalities in the dairy and beef cattle industry, but these studies typically only use one time point to compare the abundance of BRD-pathobionts between apparently healthy and BRD-affected cattle. The objective of this study was to characterize the longitudinal development of the nasopharyngeal (NP) microbiome from apparently healthy calves, and in calves with clinical signs of BRD, the microbiota dynamics from disease diagnosis to recovery.<br><br>METHODS: Deep nasopharyngeal swabs were taken from all calves immediately after transport (day 0). If a calf was diagnosed with BRD (n = 10), it was sampled, treated with florfenicol or tulathromycin, and sampled again 1, 5, and 10 days after antibiotic administration. Otherwise, healthy calves (n = 20) were sampled again on days 7 and 14. Bacterial community analysis was performed through 16S rRNA gene amplicon sequencing.<br><br>RESULTS: The NP microbiome of the healthy animals remained consistent throughout the study, regardless of time. The NP microbiota beta diversity and community composition was affected by tulathromycin or florfenicol administration. Even though BRD-pathobionts were identified by 16S rRNA gene sequencing in BRD-affected animals, no difference was observed in their relative abundance between the BRD-affected and apparently healthy animals. The abundance of BRD-pathobionts was not predictive of disease development while the relative abundance of BRD pathobionts was unique to each BRD-affected calf. Interestingly, at the end of the study period, the genera Mycoplasma was the most abundant genus in the healthy group, while Lactobacillus was the most abundant genus in the animals that recovered from BRD.<br><br>DISCUSSION: This study highlights that injected antibiotics seem to improve the NP microbiome composition (higher abundance of Lactobacillus and lower abundance of Mycoplasma), and that the relative abundance of BRD-pathobionts differs between individual calves but is not strongly predictive of BRD clinical signs, indicating that additional factors are likely important in the clinical progression of BRD.}, }
@article {pmid38033611, year = {2023}, author = {Lin, Y and Lourenco, JM and Olukosi, OA}, title = {Effects of xylanase, protease, and xylo-oligosaccharides on growth performance, nutrient utilization, short chain fatty acids, and microbiota in Eimeria-challenged broiler chickens fed high fiber diet.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {15}, number = {}, pages = {430-442}, pmid = {38033611}, issn = {2405-6383}, abstract = {A 21-d experiment was conducted to study the effect of xylanase, protease, and xylo-oligosaccharides on growth performance, nutrient utilization, gene expression of nutrient transporters, cecal short-chain fatty acids (SCFA), and cecal microbiota profile of broilers challenged with mixed Eimeria spp. The study utilized 392 zero-d-old male broiler chicks allocated to 8 treatments in a 4 × 2 factorial arrangement, as follows: corn-soybean meal diet with no enzyme (Con); Con plus xylanase alone (XYL); Con plus xylanase combined with protease (XYL + PRO); or Con plus xylo-oligosaccharides (XOS); with or without Eimeria challenge. Diets were based on a high-fiber (100 g/kg soluble fibers and 14 g/kg insoluble fibers) basal diet. At d 15, birds in challenged treatment were gavaged with a solution containing Eimeria maxima, Eimeria acervulina, and Eimeria tenella oocysts. At d 21, birds were sampled. Eimeria depressed (P < 0.01) growth performance and nutrient utilization, whereas supplementation had no effect. There were significant Eimeria × supplementation interactions for the sugar transporters GLUT5 (P = 0.02), SGLT1 (P = 0.01), SGLT4 (P < 0.01), and peptide transporter PepT1 (P < 0.01) in jejunal mucosa. Eimeria challenge increased the expression of GM-CSF2 (P < 0.01) and IL-17 (P = 0.04) but decreased (P = 0.03) IL-1β expression in the cecal tonsil. Eimeria × supplementation interactions for cecal acetate, butyrate, and total SCFA showed that concentrations increased or tended to be greater in the supplemented treatments, but only in non-challenged birds. Birds challenged with Eimeria spp. had higher concentrations of isobutyrate (P < 0.01), isovalerate (P < 0.01), and valerate (P = 0.02) in cecal content. Eimeria challenge significantly (P < 0.01) decreased the microbial richness and diversity, and increased (P < 0.01) the proportion of Anaerostipes butyraticus, Bifidobacterium pseudolongum, and Lactobacillus pontis. In conclusion, Eimeria infection depressed growth performance, nutrient utilization with regulating nutrient transporters. Furthermore, Eimeria challenge shifted the microbial profile and reduced microbial richness and diversity. On the other hand, enzyme supplementation showed limited benefits, which included increased concentrations of SCFA.}, }
@article {pmid38033603, year = {2023}, author = {Yuan, L and Zhu, C and Gu, F and Zhu, M and Yao, J and Zhu, C and Li, S and Wang, K and Hu, P and Zhang, Y and Cai, D and Liu, HY}, title = {Lactobacillus johnsonii N5 from heat stress-resistant pigs improves gut mucosal immunity and barrier in dextran sodium sulfate-induced colitis.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {15}, number = {}, pages = {210-224}, pmid = {38033603}, issn = {2405-6383}, abstract = {Developing effective strategies to prevent diarrhea and associated-gut disorders in mammals has gained great significance. Owing to the many health benefits provided by the commensal microbiota of the intestinal tract, such as against environmental perturbation, we explored the host phenotype-associated microbes and their probiotic potential. Based on the observations that the chronic heat stress-exposed weaned piglets present as heat stress-susceptible (HS-SUS) or heat stress-resistant (HS-RES) individuals, we confirmed the phenotypic difference between the two on growth performance (P < 0.05), diarrhea index (P < 0.001), intestinal heat shock protein 70 (HSP70) regulation (P < 0.01), and inflammatory responses (P < 0.01). By comparing the gut microbiome using 16S rRNA gene sequencing and KEGG functional analysis, we found that Lactobacillus johnsonii exhibited significantly higher relative abundance in the HS-RES piglets than in the HS-SUS ones (P < 0.05). Further experiments using a mouse model for chemical-induced inflammation and intestinal injury demonstrated that oral administration of a representative L. johnsonii N5 (isolated from the HS-RES piglets) ameliorated the clinical and histological signs of colitis while suppressing intestinal pro-inflammatory cytokines TNF-α and IL-6 production (P < 0.05). We found that N5 treatment enhanced tight junction proteins ZO-1 and occludin and cytoprotective HSP70 levels under physiological condition and restored their mucosal expressions in colitis (P < 0.05). In support of the high production of the anti-inflammatory cytokine IL-10, N5 promoted the intestinal Peyer's patches MHCII[+] and CD103[+] dendritic cell populations (P < 0.05), increased the regulatory T (Treg) cell numbers (P < 0.05), and decreased the Th17 population and its IL-17a production under physiological condition and during colitis (P < 0.01). Our results shed light on understanding the interaction between commensal Lactobacillus and the host health, and provide L. johnsonii N5 as an alternative to antibiotics for preventing diarrhea and intestinal diseases.}, }
@article {pmid38033594, year = {2023}, author = {Fujita, H and Ushio, M and Suzuki, K and Abe, MS and Yamamichi, M and Okazaki, Y and Canarini, A and Hayashi, I and Fukushima, K and Fukuda, S and Kiers, ET and Toju, H}, title = {Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1261137}, pmid = {38033594}, issn = {1664-302X}, abstract = {Species utilizing the same resources often fail to coexist for extended periods of time. Such competitive exclusion mechanisms potentially underly microbiome dynamics, causing breakdowns of communities composed of species with similar genetic backgrounds of resource utilization. Although genes responsible for competitive exclusion among a small number of species have been investigated in pioneering studies, it remains a major challenge to integrate genomics and ecology for understanding stable coexistence in species-rich communities. Here, we examine whether community-scale analyses of functional gene redundancy can provide a useful platform for interpreting and predicting collapse of bacterial communities. Through 110-day time-series of experimental microbiome dynamics, we analyzed the metagenome-assembled genomes of co-occurring bacterial species. We then inferred ecological niche space based on the multivariate analysis of the genome compositions. The analysis allowed us to evaluate potential shifts in the level of niche overlap between species through time. We hypothesized that community-scale pressure of competitive exclusion could be evaluated by quantifying overlap of genetically determined resource-use profiles (metabolic pathway profiles) among coexisting species. We found that the degree of community compositional changes observed in the experimental microbiome was correlated with the magnitude of gene-repertoire overlaps among bacterial species, although the causation between the two variables deserves future extensive research. The metagenome-based analysis of genetic potential for competitive exclusion will help us forecast major events in microbiome dynamics such as sudden community collapse (i.e., dysbiosis).}, }
@article {pmid38033589, year = {2023}, author = {Liu, Z and Liu, X}, title = {Gut microbiome, metabolome and alopecia areata.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1281660}, pmid = {38033589}, issn = {1664-302X}, abstract = {Alopecia areata (AA) is a type of dermatological disease characterized by rapid and non-scarring hair loss of the scalp or body skin that may be related to genetic, immunological and physiological factors. It is now believed that AA is associated with oxidative stress, autoimmune disease, neuropsychological factors, pathogens, immune checkpoint inhibitors and microecological imbalance under the premise of host genetic susceptibility. In recent years, studies have revealed the significant role of the gut microbiome or metabolome in many aspects of human health. Diverse studies have revealed that the gut microbiome and metabolome have an important influence on skin conditions. This review highlights the relationship between AA and the gut microbiome or metabolome to provide novel directions for the prevention, clinical diagnosis and treatment of AA.}, }
@article {pmid38033568, year = {2023}, author = {Seo, JY and You, SW and Gu, KN and Kim, H and Shin, JG and Leem, S and Hwang, BK and Kim, Y and Kang, NG}, title = {Longitudinal study of the interplay between the skin barrier and facial microbiome over 1 year.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1298632}, pmid = {38033568}, issn = {1664-302X}, abstract = {Skin is a diverse ecosystem that provides a habitat for microorganisms. The skin condition and the skin microbiome interact each other under diverse environmental conditions. This study was conducted on 10 study participants for a one-year, from September 2020 to August 2021, to investigate the variability of skin microbiome and skin biophysical parameters [TEWL, hydration, and elasticity (R5)] according to season, and to understand the interplay between skin microbiome and skin characteristics. We identified that Cutibacterium, Corynebacterium, Staphyloccocus, unclassified genus within Neisseriaceae, and Streptococcus were major skin microbial taxa at the genus level, and fluctuated with the seasons. Cutibacterium was more abundant in winter, while Corynebacterium, Staphylococcus, and Streptococcus were more abundant in summer. Notably, Cutibacterium and skin barrier parameter, TEWL, exhibited a co-decreasing pattern from winter to summer and showed a significant association between Cutibacterium and TEWL. Furthermore, functional profiling using KEGG provided clues on the impact of Cutibacterium on the host skin barrier. This study enhances our understanding of the skin microbiome and its interplay with skin characteristics and highlights the importance of seasonal dynamics in shaping skin microbial composition.}, }
@article {pmid38033481, year = {2023}, author = {Bai, J and Wei, JQ and Tian, Q and Xue, F and Zhang, W and He, H}, title = {The impact of electroacupuncture on anxiety-like behavior and gut microbiome in a mouse model of chronic restraint stress.}, journal = {Frontiers in behavioral neuroscience}, volume = {17}, number = {}, pages = {1292835}, pmid = {38033481}, issn = {1662-5153}, abstract = {INTRODUCTION: Electroacupuncture (EA) is a beneficial physiotherapy approach for addressing neuropsychiatric disorders. Nevertheless, the impact of EA on the gut microbiome in relation to anxiety disorders remains poorly understood.<br><br>METHODS: To address this gap, we conducted a study using a chronic restraint stress (CRS) mouse model to investigate the anti-anxiety outcome of EA and its influence on gut microbiota. Our research involved behavioral tests and comprehensive sequencing of full-length 16S rRNA microbiomes.<br><br>RESULTS: Our findings revealed that CRS led to significant anxiety-like behaviors and an imbalance in the gut microbiota. Specifically, we identified 13 species that exhibited changes associated with anxiety-like behaviors. Furthermore, EA partially alleviated both behaviors related to anxiety and the dysbiosis induced by CRS.<br><br>DISCUSSION: In summary, this study sheds light on the alterations in gut microbiota species resulting from CRS treatment and brings new light into the connection between EA's anti-anxiety effects and the gut microbiota.}, }
@article {pmid38032916, year = {2023}, author = {Sondo, M and Wonni, I and Koïta, K and Rimbault, I and Barro, M and Tollenaere, C and Moulin, L and Klonowska, A}, title = {Diversity and plant growth promoting ability of rice root-associated bacteria in Burkina-Faso and cross-comparison with metabarcoding data.}, journal = {PloS one}, volume = {18}, number = {11}, pages = {e0287084}, pmid = {38032916}, issn = {1932-6203}, abstract = {Plant-associated bacteria are essential partners in plant health and development. In addition to taking advantage of the rapid advances recently achieved in high-throughput sequencing approaches, studies on plant-microbiome interactions require experiments with culturable bacteria. A study on the rice root microbiome was recently initiated in Burkina Faso. As a follow up, the aim of the present study was to develop a collection of corresponding rice root-associated bacteria covering maximum diversity, to assess the diversity of the obtained isolates based on the culture medium used, and to describe the taxonomy, phenotype and abundance of selected isolates in the rice microbiome. More than 3,000 isolates were obtained using five culture media (TSA, NGN, NFb, PCAT, Baz). The 16S rRNA fragment sequencing of 1,013 selected isolates showed that our working collection covered four bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes) and represented 33% of the previously described diversity of the rice root microbiome at the order level. Phenotypic in vitro analysis of the plant growth promoting capacity of the isolates revealed an overall ammonium production and auxin biosynthesis capacity, while siderophore production and phosphate solubilisation were enriched in Burkholderia, Ralstonia, Acinetobacter and Pseudomonas species. Of 45 representative isolates screened for growth promotion on seedlings of two rice cultivars, five showed an ability to improve the growth of both cultivars, while five others were effective on only one cultivar. The best results were obtained with Pseudomonas taiwanensis ABIP 2315 and Azorhizobium caulinodans ABIP 1219, which increased seedling growth by 158% and 47%, respectively. Among the 14 best performing isolates, eight appeared to be abundant in the rice root microbiome dataset from previous study. The findings of this research contribute to the in vitro and in planta PGP capacities description of rice root-associated bacteria and their potential importance for plants by providing, for the first time, insight into their prevalence in the rice root microbiome.}, }
@article {pmid38032828, year = {2023}, author = {Micks, E and Reed, S and Mitchell, C}, title = {The Postmenopausal Vaginal Microbiome and Genitourinary Syndrome of Menopause.}, journal = {Clinical obstetrics and gynecology}, volume = {}, number = {}, pages = {}, pmid = {38032828}, issn = {1532-5520}, abstract = {This review summarizes our current understanding of associations of the postmenopausal vaginal microbiome with genitourinary syndrome of menopause. We review the normal postmenopausal microbiota, examine the association of the microbiome with vulvovaginal symptoms, describe microbial communities associated with physical and laboratory findings, and report the impact of different treatments for genitourinary syndrome of menopause on microbiota and symptom improvement. Postmenopausal vaginal symptoms have an underlying pathophysiology that has not been fully elucidated. Estrogen treatment may not be sufficient to relieve symptoms of vaginal discomfort in all postmenopausal individuals. In addition, other interventions targeted at changing the microbiota or pH do not consistently improve symptom severity.}, }
@article {pmid38032704, year = {2023}, author = {Lednovich, KR and Gough, S and Priyadarshini, M and Pandya, N and Nnyamah, C and Xu, K and Wicksteed, B and Mishra, S and Jain, S and Zapater, JL and Cordoba-Chacon, J and Yadav, H and Layden, B}, title = {Intestinal FFA2 promotes obesity by altering food intake in Western diet-fed mice.}, journal = {The Journal of endocrinology}, volume = {}, number = {}, pages = {}, doi = {10.1530/JOE-23-0184}, pmid = {38032704}, issn = {1479-6805}, abstract = {Short-chain fatty acids (SCFAs) are key nutrients that play a diverse set of roles in physiological function, including regulating metabolic homeostasis. Generated through the fermentation of dietary fibers in the distal colon by the gut microbiome, SCFAs and their effects are partially mediated by their cognate receptors, including free fatty acid receptor 2 (FFA2). FFA2 is highly expressed in the intestinal epithelial, where its putative functions are controversial, with numerous in vivo studies relying on global knockout mouse models to characterize intestine-specific roles of the receptor. Here, we used the Villin-Cre mouse line to generate a novel, intestine-specific knockout mouse model for FFA2 (Vil-FFA2) to investigate receptor function within the intestine. Because dietary changes are known to affect the composition of the gut microbiome, and can thereby alter SCFA production, we performed an obesogenic challenge on male Vil-FFA2 mice and their littermate controls (FFA2-floxed, FFA2fl/fl) to identify physiological changes on a high-fat, high-sugar "Western diet" (WD) compared to a low-fat control diet (CD). We found that the WD-fed Vil-FFA2 mice were transiently protected from the obesogenic effects of the WD, and had lower fat mass and improved glucose homeostasis compared to the WD-fed FFA2fl/fl control group during the first half of the study. Additionally, major differences in respiratory exchange ratio and energy expenditure were observed in the WD-fed Vil-FFA2 mice, and food intake was found to be significantly reduced at multiple points in the study. Taken together, this study uncovers a novel role of intestinal FFA2 in mediating the development of obesity.}, }
@article {pmid38032526, year = {2023}, author = {Dong, X and Deng, L and Su, Y and Han, X and Yao, S and Wu, W and Cao, J and Tian, L and Bai, Y and Wang, G and Ren, W}, title = {Curcumin alleviates traumatic brain injury induced by gas explosion through modulating gut microbiota and suppressing the LPS/TLR4/MyD88/NF-κB pathway.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {38032526}, issn = {1614-7499}, support = {U2004102//National Natural Science Foundation of China/ ; U1904209//National Natural Science Foundation of China/ ; 232102311071//Henan Provincial Science and Technology Research Project/ ; 202300410312//Natural Science Foundation of Henan Province/ ; }, abstract = {Gas explosions (GE) are a prevalent and widespread cause of traumatic brain injury (TBI) in coal miners. However, the impact and mechanism of curcumin on GE-induced TBI in rats remain unclear. In this study, we simulated GE-induced TBI in rats and administered curcumin orally at a dose of 100 mg/kg every other day for 7 days to modulate the gut microbiota in TBI rats. We employed 16S rRNA sequencing and LC-MS/MS metabolomic analysis to investigate changes in the intestinal flora and its metabolic profile. Additionally, we utilized ELISA, protein assays, and immunohistochemistry to assess neuroinflammatory signaling molecules for validation. In a rat TBI model, GE resulted in weight loss, pathological abnormalities, and cortical hemorrhage. Treatment with curcumin significantly mitigated histological abnormalities and microscopic mitochondrial structural changes in brain tissue. Furthermore, curcumin treatment markedly ameliorated GE-induced brain dysfunction by reducing the levels of several neuroinflammatory signaling molecules, including neuron-specific enolase, interleukin (IL)-1β, IL-6, and cryptothermic protein 3. Notably, curcumin reshaped the gut microbiome by enhancing evenness, richness, and composition. Prevotella_9, Alloprevotella, Bacilli, Lactobacillales, Proteobacteria, and Gammaproteobacteria were identified as prominent members of the gut microbiota, increasing the linear discriminant analysis scores and specifically enhancing the abundance of bacteria involved in the nuclear factor (NF)-κB signaling pathway, such as Lachnospiraceae and Roseburia. Additionally, there were substantial alterations in serum metabolites associated with metabolic NF-κB signaling pathways in the model group. Curcumin administration reduced serum lipopolysaccharide levels and downregulated downstream Toll-like receptor (TLR)4/myeloid differentiation primary response 88 (MyD88)/NF-κB signaling. Furthermore, curcumin alleviated GE-induced TBI in rats by modulating the gut microbiota and its metabolites. Based on these protective effects, curcumin may exert its influence on the gut microbiota and the TLR4/MyD88/NF-κB signaling pathways to ameliorate GE-induced TBI.}, }
@article {pmid38032332, year = {2023}, author = {Zawadzka-Głos, L}, title = {Microbiota and antibiotic therapy in rhinosinusitis.}, journal = {Otolaryngologia polska = The Polish otolaryngology}, volume = {77}, number = {5}, pages = {36-42}, doi = {10.5604/01.3001.0053.8709}, pmid = {38032332}, issn = {2300-8423}, mesh = {Humans ; *Sinusitis/drug therapy ; Anti-Bacterial Agents/therapeutic use ; *Microbiota ; *Nasal Polyps ; }, abstract = {Rhinosinusitis is one of the most frequently diagnosed diseases in patients seeking medical consultation. Sinusitis is a heterogeneous group of diseases and can be acute or chronic. The current state of knowledge on rhinosinusitis is presented in the recommendations of the European Position Paper on Rhinosynusitis and Nasal Polyps 2020 (EPOS 2020). More and more attention is paid to the condition of the microbiota in the context of inflammatory changes in the sinuses. There is also a negative effect of excessively prescribed antibiotics on the increase in bacterial resistance to drugs and significant changes in the disturbance in the composition of the microbiota during antibiotic therapy. Since the most common etiology of acute sinusitis is viral, the use of antibiotics in uncomplicated sinusitis is unjustified. New therapeutic solutions are sought, including the use of herbal medicines. The EPOS 2020 document recommends the use of BNO 1016 in uncomplicated acute rhinosinusitis. New models of treatment also take into account the use of biological drugs, especially in the treatment of chronic rhinosinusitis.}, }
@article {pmid38032239, year = {2023}, author = {Bowen, M and Farag, IF and Main, CR and Biddle, JF}, title = {Reference library for microbial source tracking in the mid-Atlantic United States.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0067423}, doi = {10.1128/MRA.00674-23}, pmid = {38032239}, issn = {2576-098X}, abstract = {Microbial source tracking can determine fecal contamination but requires a relevant, sizable reference library for analysis. We provide a reference library of 100+ fecal microbiome samples relevant to mid-Atlantic United States ecosystems. Included are wild and domesticated fauna, wastewater, and septic samples applicable to Delaware source tracking studies.}, }
@article {pmid38032203, year = {2023}, author = {Tahiri, M and Johnsrud, C and Steffensen, IL}, title = {Evidence and hypotheses on adverse effects of the food additives carrageenan (E 407)/processed Eucheuma seaweed (E 407a) and carboxymethylcellulose (E 466) on the intestines: a scoping review.}, journal = {Critical reviews in toxicology}, volume = {}, number = {}, pages = {1-51}, doi = {10.1080/10408444.2023.2270574}, pmid = {38032203}, issn = {1547-6898}, abstract = {This scoping review provides an overview of publications reporting adverse effects on the intestines of the food additives carrageenan (CGN) (E 407)/processed Eucheuma seaweed (PES) (E 407a) and carboxymethylcellulose (CMC) (E 466). It includes evidence from human, experimental mammal and in vitro research publications, and other evidence. The databases Medline, Embase, Scopus, Web of Science Core Collection, Cochrane Database of Systematic Reviews and Epistemonikos were searched without time limits, in addition to grey literature. The publications retrieved were screened against predefined criteria. From two literature searches, 2572 records were screened, of which 224 records were included, as well as 38 records from grey literature, making a total of 262 included publications, 196 on CGN and 101 on CMC. These publications were coded and analyzed in Eppi-Reviewer and data gaps presented in interactive maps. For CGN, five, 69 and 33 research publications on humans, experimental mammals and in vitro experiments were found, further separated as degraded or native (non-degraded) CGN. For CMC, three human, 20 animal and 14 in vitro research publications were obtained. The most studied adverse effects on the intestines were for both additives inflammation, the gut microbiome, including fermentation, intestinal permeability, and cancer and metabolic effects, and immune effects for CGN. Further studies should focus on native CGN, in the form and molecular weight used as food additive. For both additives, randomized controlled trials of sufficient power and with realistic dietary exposure levels of single additives, performed in persons of all ages, including potentially vulnerable groups, are needed.}, }
@article {pmid38031529, year = {2023}, author = {Sanders, WB}, title = {The disadvantages of current proposals to redefine lichens: A comment on Hawksworth &amp; Grube (2020): 'Lichens redefined as complex ecosystems'.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.19321}, pmid = {38031529}, issn = {1469-8137}, }
@article {pmid38031491, year = {2023}, author = {Kim, SH and Choi, Y and Oh, J and Lim, EY and Lee, JE and Song, EJ and Nam, YD and Kim, H}, title = {Associations among the Duodenal Ecosystem, Gut Microbiota, and Nutrient Intake in Functional Dyspepsia.}, journal = {Gut and liver}, volume = {}, number = {}, pages = {}, doi = {10.5009/gnl230130}, pmid = {38031491}, issn = {2005-1212}, abstract = {BACKGROUND/AIMS: : Functional dyspepsia (FD) has long been regarded as a syndrome because its pathophysiology is multifactorial. However, recent reports have provided evidence that changes in the duodenal ecosystem may be the key. This study aimed to identify several gastrointestinal factors and biomarkers associated with FD, specifically changes in the duodenal ecosystem that may be key to understanding its pathophysiology.<br><br>METHODS: : In this case-control study, 28 participants (12 with FD and 16 healthy control individuals) were assessed for dietary nutrients, gastrointestinal symptom severity, immunological status of the duodenal mucosa, and microbiome composition from oral, duodenal, and fecal samples. Integrated data were analyzed using immunohistochemistry, real-time polymerase chain reaction, 16S rRNA sequencing, and network analysis.<br><br>RESULTS: : Duodenal mucosal inflammation and impaired expression of tight junction proteins were confirmed in patients with FD. The relative abundance of duodenal Streptococcus (p=0.014) and reductions in stool Butyricicoccus (p=0.047) were confirmed. These changes in the gut microbiota were both correlated with symptom severity. Changes in dietary micronutrients, such as higher intake of valine, were associated with improved intestinal barrier function and microbiota.<br><br>CONCLUSIONS: : This study emphasizes the relationships among dietary nutrition, oral and gut microbiota, symptoms of FD, impaired function of the duodenal barrier, and inflammation. Assessing low-grade inflammation or increased permeability in the duodenal mucosa, along with changes in the abundance of stool Butyricicoccus, is anticipated to serve as effective biomarkers for enhancing the objectivity of FD diagnosis and monitoring.}, }
@article {pmid38031487, year = {2023}, author = {Hawksworth, DL and Grube, M}, title = {Reflections on lichens as ecosystems.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.19418}, pmid = {38031487}, issn = {1469-8137}, }
@article {pmid38031339, year = {2023}, author = {Kamenova, S and de Muinck, EJ and Veiberg, V and Utsi, TA and Steyaert, SMJG and Albon, SD and Loe, LE and Trosvik, P}, title = {Gut microbiome biogeography in reindeer supersedes millennia of ecological and evolutionary separation.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiad157}, pmid = {38031339}, issn = {1574-6941}, abstract = {Ruminants are dependent on their gut microbiomes for nutrient extraction from plant diets. However, knowledge about the composition, diversity, function, and spatial structure of gut microbiomes, especially in wild ruminants, is limited, largely because analysis has been restricted to faeces or the rumen. In two geographically separated reindeer subspecies, 16S rRNA gene amplicon sequencing revealed strong spatial structuring, and pronounced differences in microbial diversity of at least 33 phyla across the stomach, small intestine, and large intestine (including faeces). The main structural feature was the Bacteroidota to Firmicutes ratio, which declined from the stomachs to the large intestine, likely reflecting functional adaptation. Metagenome shotgun sequencing also revealed highly significant structuring in the relative occurrence of carbohydrate-active enzymes (CAZymes). CAZymes were enriched in the rumen relative to the small and large intestine. Interestingly, taxonomic diversity was highest in the large intestine, suggesting an important and understudied role for this organ. Despite the two study populations being separated by an ocean and six millennia of evolutionary history, gut microbiome structuring was remarkably consistent. Our study suggests a strong selection for gut microbiome biogeography along the gastrointestinal tract in reindeer subspecies.}, }
@article {pmid38031252, year = {2023}, author = {Crossland, NA and Beck, S and Tan, WY and Lo, M and Mason, JB and Zhang, C and Guo, W and Crott, JW}, title = {Fecal microbiota transplanted from old mice promotes more colonic inflammation, proliferation, and tumor formation in azoxymethane-treated A/J mice than microbiota originating from young mice.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2288187}, doi = {10.1080/19490976.2023.2288187}, pmid = {38031252}, issn = {1949-0984}, abstract = {Aging is a strong risk factor for colorectal cancer (CRC). It is well established that gut microbial dysbiosis can play a role in the etiology of CRC. Although the composition of the gut microbial community changes with age and is reported to become more pro-inflammatory, it is unclear whether such changes are also pro-tumorigenic for the colon. To address this gap, we conducted fecal microbiota transplants (FMT) from young (DY, ~6 wk) and old (DO, ~72 wk) donor mice into young (8 wk) recipient mice that were pre-treated with antibiotics. After initiating tumorigenesis with azoxymethane, recipients were maintained for 19 wk during which time they received monthly FMT boosters. Compared to recipients of young donors (RY), recipients of old donors (RO) had an approximately 3-fold higher prevalence of histologically confirmed colon tumors (15.8 vs 50%, Chi2 P = .03), approximately 2-fold higher proliferating colonocytes as well as significantly elevated colonic IL-6, IL-1β and Tnf-α. Transcriptomics analysis of the colonic mucosa revealed a striking upregulation of mitochondria-related genes in the RO mice, a finding corroborated by increased mitochondrial abundance. Amongst the differences in fecal microbiome observed between DY and DO mice, the genera Ruminoclostridium, Lachnoclostridium and Marvinbryantia were more abundant in DY mice while the genera Bacteroides and Akkermansia were more abundant in DO mice. Amongst recipients, Ruminoclostridium and Lachnoclostridium were higher in RY mice while Bacteroides was higher in RO mice. Differences in fecal microbiota were observed between young and old mice, some of which persisted upon transplant into recipient mice. Recipients of old donors displayed significantly higher colonic proliferation, inflammation and tumor abundance compared to recipients of young donors. These findings support an etiological role for altered gut microbial communities in the increased risk for CRC with increasing age and establishes that such risk can be transmitted between individuals.}, }
@article {pmid38031142, year = {2023}, author = {Holm, JB and France, MT and Gajer, P and Ma, B and Brotman, RM and Shardell, M and Forney, L and Ravel, J}, title = {Integrating compositional and functional content to describe vaginal microbiomes in health and disease.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {259}, pmid = {38031142}, issn = {2049-2618}, support = {R01-NR015495/NR/NINR NIH HHS/United States ; }, abstract = {BACKGROUND: A Lactobacillus-dominated vaginal microbiome provides the first line of defense against adverse genital tract health outcomes. However, there is limited understanding of the mechanisms by which the vaginal microbiome modulates protection, as prior work mostly described its composition through morphologic assessment and marker gene sequencing methods that do not capture functional information. To address this gap, we developed metagenomic community state types (mgCSTs) which use metagenomic sequences to describe and define vaginal microbiomes based on both composition and functional potential.<br><br>RESULTS: MgCSTs are categories of microbiomes classified using taxonomy and the functional potential encoded in their metagenomes. MgCSTs reflect unique combinations of metagenomic subspecies (mgSs), which are assemblages of bacterial strains of the same species, within a microbiome. We demonstrate that mgCSTs are associated with demographics such as age and race, as well as vaginal pH and Gram stain assessment of vaginal smears. Importantly, these associations varied between mgCSTs predominated by the same bacterial species. A subset of mgCSTs, including three of the six predominated by Gardnerella vaginalis mgSs, as well as mgSs of L. iners, were associated with a greater likelihood of bacterial vaginosis diagnosed by Amsel clinical criteria. This L. iners mgSs, among other functional features, encoded enhanced genetic capabilities for epithelial cell attachment that could facilitate cytotoxin-mediated cell lysis. Finally, we report a mgSs and mgCST classifier for which source code is provided and may be adapted for use by the microbiome research community.<br><br>CONCLUSIONS: MgCSTs are a novel and easily implemented approach to reduce the dimension of complex metagenomic datasets while maintaining their functional uniqueness. MgCSTs enable the investigation of multiple strains of the same species and the functional diversity in that species. Future investigations of functional diversity may be key to unraveling the pathways by which the vaginal microbiome modulates the protection of the genital tract. Importantly, our findings support the hypothesis that functional differences between vaginal microbiomes, including those that may look compositionally similar, are critical considerations in vaginal health. Ultimately, mgCSTs may lead to novel hypotheses concerning the role of the vaginal microbiome in promoting health and disease, and identify targets for novel prognostic, diagnostic, and therapeutic strategies to improve women's genital health. Video Abstract.}, }
@article {pmid38031016, year = {2023}, author = {Li, P and Jiang, J and Li, Y and Lan, Y and Yang, F and Wang, J and Xie, Y and Xiong, F and Wu, J and Liu, H and Fan, Z}, title = {Metagenomic analysis reveals distinct changes in the gut microbiome of obese Chinese children.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {721}, pmid = {38031016}, issn = {1471-2164}, support = {No. 2023YFS0034 and 2020YFS0109//the Science and Technology Bureau of Sichuan Province/ ; No. KL119//the Clinical Discipline Development Fund of West China Second Hospital, Sichuan University/ ; SCU2022D022//the Fundamental Research Funds for the Central Universities/ ; }, abstract = {BACKGROUND: The prevalence of obese children in China is increasing, which poses a great challenge to public health. Gut microbes play an important role in human gut health, and changes in gut status are closely related to obesity. However, how gut microbes contribute to obesity in children remains unclear. In our study, we performed shotgun metagenomic sequencing of feces from 23 obese children, 8 overweight children and 22 control children in Chengdu, Sichuan, China.<br><br>RESULTS: We observed a distinct difference in the gut microbiome of obese children and that of controls. Compared with the controls, bacterial pathogen Campylobacter rectus was significantly more abundant in obese children. In addition, functional annotation of microbial genes revealed that there might be gut inflammation in obese children. The guts of overweight children might belong to the transition state between obese and control children due to a gradient in relative abundance of differentially abundant species. Finally, we compared the gut metagenomes of obese Chinese children and obese Mexican children and found that Trichuris trichiura was significantly more abundant in the guts of obese Mexican children.<br><br>CONCLUSIONS: Our results contribute to understanding the changes in the species and function of intestinal microbes in obese Chinese children.}, }
@article {pmid38030903, year = {2023}, author = {Lutz, S and Bodenhausen, N and Hess, J and Valzano-Held, A and Waelchli, J and Deslandes-Hérold, G and Schlaeppi, K and van der Heijden, MGA}, title = {Soil microbiome indicators can predict crop growth response to large-scale inoculation with arbuscular mycorrhizal fungi.}, journal = {Nature microbiology}, volume = {8}, number = {12}, pages = {2277-2289}, pmid = {38030903}, issn = {2058-5276}, support = {GRS-072/17//Gebert R&#xfc;f Stiftung (Gebert R&#xfc;f Foundation)/ ; GRS-088/20//Gebert R&#xfc;f Stiftung (Gebert R&#xfc;f Foundation)/ ; GRS-072/17//Gebert R&#xfc;f Stiftung (Gebert R&#xfc;f Foundation)/ ; 40IN40_215832 / 1//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 40IN40_215832 / 1//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 40IN40_215832 / 1//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, abstract = {Alternative solutions to mineral fertilizers and pesticides that reduce the environmental impact of agriculture are urgently needed. Arbuscular mycorrhizal fungi (AMF) can enhance plant nutrient uptake and reduce plant stress; yet, large-scale field inoculation trials with AMF are missing, and so far, results remain unpredictable. We conducted on-farm experiments in 54 fields in Switzerland and quantified the effects on maize growth. Growth response to AMF inoculation was highly variable, ranging from -12% to +40%. With few soil parameters and mainly soil microbiome indicators, we could successfully predict 86% of the variation in plant growth response to inoculation. The abundance of pathogenic fungi, rather than nutrient availability, best predicted (33%) AMF inoculation success. Our results indicate that soil microbiome indicators offer a sustainable biotechnological perspective to predict inoculation success at the beginning of the growing season. This predictability increases the profitability of microbiome engineering as a tool for sustainable agricultural management.}, }
@article {pmid38030898, year = {2023}, author = {Gancz, AS and Farrer, AG and Nixon, MP and Wright, S and Arriola, L and Adler, C and Davenport, ER and Gully, N and Cooper, A and Britton, K and Dobney, K and Silverman, JD and Weyrich, LS}, title = {Ancient dental calculus reveals oral microbiome shifts associated with lifestyle and disease in Great Britain.}, journal = {Nature microbiology}, volume = {8}, number = {12}, pages = {2315-2325}, pmid = {38030898}, issn = {2058-5276}, support = {DGE1255832//National Science Foundation (NSF)/ ; DGE1255832//National Science Foundation (NSF)/ ; }, abstract = {The prevalence of chronic, non-communicable diseases has risen sharply in recent decades, especially in industrialized countries. While several studies implicate the microbiome in this trend, few have examined the evolutionary history of industrialized microbiomes. Here we sampled 235 ancient dental calculus samples from individuals living in Great Britain (∼2200 BCE to 1853 CE), including 127 well-contextualized London adults. We reconstructed their microbial history spanning the transition to industrialization. After controlling for oral geography and technical biases, we identified multiple oral microbial communities that coexisted in Britain for millennia, including a community associated with Methanobrevibacter, an anaerobic Archaea not commonly prevalent in the oral microbiome of modern industrialized societies. Calculus analysis suggests that oral hygiene contributed to oral microbiome composition, while microbial functions reflected past differences in diet, specifically in dairy and carbohydrate consumption. In London samples, Methanobrevibacter-associated microbial communities are linked with skeletal markers of systemic diseases (for example, periostitis and joint pathologies), and their disappearance is consistent with temporal shifts, including the arrival of the Second Plague Pandemic. This suggests pre-industrialized microbiomes were more diverse than previously recognized, enhancing our understanding of chronic, non-communicable disease origins in industrialized populations.}, }
@article {pmid38030815, year = {2023}, author = {Zhang, N and Zhu, W and Zhang, S and Liu, T and Gong, L and Wang, Z and Zhang, W and Cui, Y and Wu, Q and Li, J and Yu, H and El-Omar, EM and Hao, J and Lu, W}, title = {A Novel Bifidobacterium/Klebsiella Ratio in Characterization Analysis of the Gut and Bile Microbiota of CCA Patients.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {5}, pmid = {38030815}, issn = {1432-184X}, abstract = {Cholangiocarcinoma (CCA) is a serious health problem worldwide. The gut and bile microbiota have not been clearly characterized in patients with CCA, and better noninvasive diagnostic approaches for CCA need to be established. The aim of this study was to investigate the characteristics of the gut and bile microbiota in CCA patients. Forty-two CCA patients and 16 healthy normal controls (HNCs) were enrolled. DNA was extracted from fecal and bile samples and subjected to 16S rRNA gene analysis. We found that there were significant differences in the species diversity, structure, and composition of the microbial communities between the CCA group and the HNC grouAt the phylum level, compared with that in the HNC group, the relative abundance of Firmicutes and Actinobacteriota was significantly decreased in the CCA group, whereas Proteobacteria and Bacteroidota were significantly enriched. The Firmicutes/Bacteroidota (F/B) ratio significantly decreased in the CCA group compared to the HNC grouThe relative abundance of Klebsiella in the CCA group was significantly higher than that in the HNC group, while the relative abundance of Bifidobacterium was significantly decreased. The Bifidobacterium/Klebsiella (B/K) ratio was established as a novel biomarker and was found to be significantly decreased in the CCA group compared with the HNC grouOur findings provide evidence supporting the use of Klebsiella and Bifidobacterium as noninvasive intestinal microbiomarkers for improving the diagnosis of CCA.}, }
@article {pmid38030736, year = {2023}, author = {Gajecka, M and Gutaj, P and Jaskiewicz, K and Rydzanicz, M and Szczapa, T and Kaminska, D and Kosewski, G and Przyslawski, J and Ploski, R and Wender-Ozegowska, E}, title = {Effects of maternal type 1 diabetes and confounding factors on neonatal microbiomes.}, journal = {Diabetologia}, volume = {}, number = {}, pages = {}, pmid = {38030736}, issn = {1432-0428}, support = {PSNC-534//Poznan Supercomputing and Networking Center/ ; Professor Artur Czy&#x17c;yk' Scientific Grant 2015//Polish Diabetes Association/ ; Professor Artur Czy&#x17c;yk' Scientific Grant 2017//Polish Diabetes Association/ ; 502-01-01110142-05618//Uniwersytet Medyczny im. Karola Marcinkowskiego w Poznaniu/ ; 502-14-03301402-09911//Uniwersytet Medyczny im. Karola Marcinkowskiego w Poznaniu/ ; }, abstract = {AIMS/HYPOTHESIS: Body niche-specific microbiota in maternal-neonatal dyads from gravidae with type 1 diabetes have not been quantitatively and functionally examined. Similarly, the impact of pregnancy-specific factors, such as the presence of comorbidities known to occur more frequently among gravidae with type 1 diabetes, including Caesarean delivery, as well as antibiotic prophylaxis, level of glycaemic control during each trimester of pregnancy and insulin administration, has not been adequately considered. The aims of this study were to characterise the maternal and neonatal microbiomes, assess aspects of microbiota transfer from the maternal microbiomes to the neonatal microbiome and explore the impact of type 1 diabetes and confounding factors on the microbiomes.<br><br>METHODS: In this observational case-control study, we characterised microbiome community composition and function using 16S rRNA amplicon sequencing in a total of 514 vaginal, rectal and ear-skin swabs and stool samples derived from 92 maternal-neonatal dyads (including 50 gravidae with type 1 diabetes) and in-depth clinical metadata from throughout pregnancy and delivery.<br><br>RESULTS: Type 1 diabetes-specific microbiota were identified among gravidae with type 1 diabetes and their neonates. Neonatal microbiome profiles of ear-skin swabs and stool samples were established, indicating the taxa more prevalent among neonates born to mothers with type 1 diabetes compared with neonates born to control mothers. Without taking into account the type 1 diabetes status of mothers, both delivery mode and intrapartum antibiotic prophylaxis were found to have an influence on neonatal microbiota composition (both p=0.001). In the logistic regression analysis involving all confounding variables, neonatal ear-skin microbiome variation was explained by maternal type 1 diabetes status (p=0.020) and small for gestational age birthweight (p=0.050). Moreover, in women with type 1 diabetes, a relationship was found between HbA1c levels >55 mmol/mol (>7.2%) measured in the first trimester of pregnancy and neonatal ear-skin microbiota composition (p=0.008). In the PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) assessment, pathways concerning carbohydrate biosynthesis were predicted as key elements of the microbial functional profiles dysregulated in type 1 diabetes. Additionally, in SourceTracker analysis, we found that, on average, 81.0% of neonatal microbiota was attributed to maternal sources. An increase in the contribution of maternal rectum microbiota and decrease in the contribution of maternal cervix microbiota were found in ear-skin samples of vaginally delivered neonates of mothers with type 1 diabetes compared with neonates born to control mothers (83.2% vs 59.5% and 0.7% vs 5.2%, respectively).<br><br>CONCLUSIONS/INTERPRETATION: These findings indicate that, in addition to maternal type 1 diabetes, glycaemic dysregulation before/in the first trimester of pregnancy, mode of delivery and intrapartum antibiotic prophylaxis may contribute to the inoculation and formation of the neonatal microbiomes.<br><br>DATA AVAILABILITY: The BioProject (PRJNA961636) and associated SRA metadata are available at http://www.ncbi.nlm.nih.gov/bioproject/961636 . Processed data on probiotic supplementation and the PICRUSt analysis are available in the Mendeley Data Repository (https://doi.org/10.17632/g68rwnnrfk.1).}, }
@article {pmid38030652, year = {2023}, author = {Bacci, G and Meriggi, N and Cheng, CLY and Ng, KH and Iannucci, A and Mengoni, A and Cavalieri, D and Cannicci, S and Fratini, S}, title = {Species-specific gill's microbiome of eight crab species with different breathing adaptations.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {21033}, pmid = {38030652}, issn = {2045-2322}, support = {207080320.088562.26020.430.01//Hong Kong Government/ ; 260008686.088562.26000.400.01//TUYF Charitable Trust funds, Hong Kong/ ; CN00000033//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca/ ; }, abstract = {Transitions to physically different environments, such as the water-to-land transition, proved to be the main drivers of relevant evolutionary events. Brachyuran crabs evolved remarkable morphological, behavioral, and physiological adaptations to terrestrial life. Terrestrial species evolved new respiratory structures devoted to replace or support the gills, a multifunctional organ devoted to gas exchanges, ion-regulation and nitrogen excretion. It was hypothesized that microorganisms associated with respiratory apparatus could have facilitated the processes of osmoregulation, respiration, and elimination of metabolites along this evolutionary transition. To test if crab species with different breathing adaptations may host similar microbial communities on their gills, we performed a comparative targeted-metagenomic analysis, selecting two marine and six terrestrial crabs belonging to different families and characterised by different breathing adaptations. We analysed anterior and posterior gills separately according to their different and specific roles. Regardless of their terrestrial or marine adaptations, microbial assemblages were strongly species-specific indicating a non-random association between the host and its microbiome. Significant differences were found in only two terrestrial species when considering posterior vs. anterior gills, without any association with species-specific respiratory adaptations. Our results suggest that all the selected species are strongly adapted to the ecological niche and specific micro-habitat they colonise.}, }
@article {pmid38030540, year = {2023}, author = {Holers, VM}, title = {Are there causal mucosal drivers in the preclinical development of rheumatoid arthritis?.}, journal = {Seminars in arthritis and rheumatism}, volume = {}, number = {}, pages = {152324}, doi = {10.1016/j.semarthrit.2023.152324}, pmid = {38030540}, issn = {1532-866X}, abstract = {BACKGROUND: The causal pathways which drive the development of seropositive rheumatoid arthritis (RA) are incompletely understood, especially in the period of time prior to the first development of signs and symptoms of joint involvement. That asymptomatic period, designated herein as pre-RA, is characterized by the presence of RA-related autoantibodies for many years and is the subject of an increasing number of studies as well as a focus of efforts to prevent the onset of clinically apparent arthritis.<br><br>OBJECTIVES: To review the potential causal pathways in pre-RA by examining results of studies which evaluate the systemic peripheral blood and mucosal alterations that have been identified in individuals who are genetically at-risk, and/or who elaborate RA-related autoantibodies, and are defined as in a pre-RA period.<br><br>METHODS: Published studies by the author and his colleagues, as well as publications by other groups, which describe the presence of biomarkers at mucosal sites and in the blood were reviewed. From these studies, a hypothesis related to the presence of pre-RA causal drivers was constructed.<br><br>RESULTS: The author and his colleagues, as well as other groups, have shown that there are multiple mucosal sites, primarily gut, lung and oral/peridontial, which appear in subsets of individuals in the pre-RA to exhibit inflammation and/or the presence of local production of IgA and IgG RA-related autoantibodies, including anti-citrullinated protein antibodies (ACPA). These findings are reviewed herein. There remain a large number of unanswered questions, though, related to the immune mechanisms that are operative at each site, as well as how these local findings evolve to causal systemic autoimmunity and eventually inflammatory arthritis.<br><br>AUTHOR'S CONCLUSIONS: Comprehensive natural history studies are required to understand how multiple mucosal sites which appear to be involved in pre-RA are causally involved in the development of arthritis. Questions remain as to whether there are independent, serially involved, or inter-related causal immune pathways originating from these sites. In addition, the microbiota which may be involved in local immune inflammation and autoantibody production should be identified and characterized.}, }
@article {pmid38030382, year = {2023}, author = {Song, CH and Kim, N and Nam, RH and Choi, SI and Jang, JY and Kim, EH and Choi, J and Choi, Y and Yoon, H and Lee, SM}, title = {The Possible Preventative Role of Lactate- and Butyrate-Producing Bacteria in Colorectal Carcinogenesis.}, journal = {Gut and liver}, volume = {}, number = {}, pages = {}, doi = {10.5009/gnl230385}, pmid = {38030382}, issn = {2005-1212}, abstract = {BACKGROUND/AIMS: : The gut microbiome has emerged as a key player that mechanistically links various risk factors to colorectal cancer (CRC) etiology. However, the role of the gut microbiome in CRC pathogenesis remains unclear. This study aimed to characterize the gut microbiota in healthy controls (HCs) and patients with colorectal adenoma (AD) and CRC in subgroups based on sex and age.<br><br>METHODS: : Study participants who visited the hospital for surveillance of CRC or gastrointestinal symptoms were prospectively enrolled, and the gut microbiome was analyzed based on fecal samples.<br><br>RESULTS: : In terms of HC-AD-CRC sequence, commensal bacteria, including lactate-producing (Streptococcus salivarius) and butyrate-producing (Faecalibacterium prausnitzii, Anaerostipes hadrus, and Eubacterium hallii) bacteria, were more abundant in the HC group than in the AD and CRC groups. In the sex comparison, the female HC group had more lactate-producing bacteria (Bifidobacterium adolescentis, Bifidobacterium catenulatum, and Lactobacillus ruminis) than the male HC group. In age comparison, younger subjects had more butyrate-producing bacteria (Agathobaculum butyriciproducens and Blautia faecis) than the older subjects in the HC group. Interestingly, lactate-producing bacteria (B. catenulatum) were more abundant in females than males among younger HC group subjects. However, these sex- and age-dependent differences were not observed in the AD and CRC groups.<br><br>CONCLUSIONS: : The gut microbiome, specifically lactate- and butyrate-producing bacteria, which were found to be abundant in the HC group, may play a role in preventing the progression of CRC. In particular, lactate-producing bacteria, which were found to be less abundant in healthy male controls may contribute to the higher incidence of CRC in males.}, }
@article {pmid38030126, year = {2023}, author = {Ahsan, T and Tian, PC and Gao, J and Wang, C and Liu, C and Huang, YQ}, title = {Effects of microbial agent and microbial fertilizer input on soil microbial community structure and diversity in a peanut continuous cropping system.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2023.11.028}, pmid = {38030126}, issn = {2090-1224}, abstract = {INTRODUCTION: The soil harbors a diverse array of microorganisms, and these are essential components of terrestrial ecosystems. The presence of microorganisms in the soil, particularly in the rhizosphere, is closely linked to plant growth and soil fertility.<br><br>OBJECTIVE: The primary objective of this study is to assess the potential advantages of integrating microbial inoculants with compound fertilizer in enhancing peanut yield.<br><br>METHODS: We utilized Illumina MiSeq high-throughput sequencing technology to conduct our investigation. The experimental design consists of four treatment groups: compound fertilizers (CF), compound fertilizers supplemented with microbial agents (CF+MA), compound fertilizers supplemented with microbial fertilizers (CF+MF), and compound fertilizers supplemented with both microbial agents and microbial fertilizers (CF+MM).<br><br>RESULTS: The experimental results demonstrated a significant increase in peanut yield upon application of CF+MA, CF+MF, and CF+MM treatments. During the blossom stage and pod-setting stage, the soil's catalase, urease, and acid phosphatase activities were significantly increased in the CF+MA, and CF+MM treatments compared to the CF treatment. The application of CF+MA resulted in an increase in bacterial richness in the rhizosphere soil of peanuts, as indicated by the sequencing results. The application of CF+MA, CF+MF, and CF+MM resulted in a reduction of fungal diversity. Proteobacteria, Actinobacteria, and Acidobacteria were the dominant bacterial phyla, while Ascomycota and Basidiomycota were the dominant phyla in the fungal component of the rhizosphere soil microbiome across all experimental treatments.<br><br>CONCLUSION: Microbial agents and fertilizers modify the peanut rhizosphere soil's microbial community structure, as per our findings. The abundance of potentially beneficial bacteria (Bradyrhizobium, Rhizobium, and Burkholderia) and fungi (Trichoderma and Cladophialophora) could increase, while pathogenic fungi (Penicillium and Fusarium) decreased, thereby significantly promoting plant growth and yield of peanut.}, }
@article {pmid38030048, year = {2023}, author = {Gong, X and Ma, Y and Deng, X and Li, A and Li, X and Kong, X and Liu, Y and Liu, X and Guo, K and Yang, Y and Li, Z and Wei, H and Zhou, D and Hong, Z}, title = {Intestinal dysbiosis exacerbates susceptibility to the anti-NMDA receptor encephalitis-like phenotype by changing blood brain barrier permeability and immune homeostasis.}, journal = {Brain, behavior, and immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.bbi.2023.11.030}, pmid = {38030048}, issn = {1090-2139}, abstract = {Changes in the intestinal microbiota have been observed in patients with anti-N-methyl-D-aspartate receptor encephalitis (NMDARE). However, whether and how the intestinal microbiota is involved in the pathogenesis of NMDARE susceptibility needs to be demonstrated. Here, we first showed that germ-free (GF) mice that underwent fecal microbiota transplantation (FMT) from NMDARE patients, whose fecal microbiota exhibited low short-chain fatty acid content, decreased abundance of Lachnospiraceae, and increased abundance of Verrucomicrobiota, Akkermansia, Parabacteroides, Oscillospirales, showed significant behavioral deficits. Then, these FMT mice were actively immunized with an amino terminal domain peptide from the GluN1 subunit (GluN1356-385) to mimic the pathogenic process of NMDARE. We found that FMT mice showed an increased susceptibility to an encephalitis-like phenotype characterized by more clinical symptoms, greater pentazole (PTZ)-induced susceptibility to seizures, and higher levels of T2 weighted image (T2WI) hyperintensities following immunization. Furthermore, mice with dysbiotic microbiota had impaired blood-brain barrier integrity and a proinflammatory condition. In NMDARE-microbiota recipient mice, the levels of Evan's blue (EB) dye extravasation increased, ZO-1 and claudin-5 expression decreased, and the levels of proinflammatory cytokines (IL-1, IL-6, IL-17, TNF-α and LPS) increased. Finally, significant brain inflammation, mainly in hippocampal and cortical regions, with modest neuroinflammation, immune cell infiltration, and reduced expression of NMDA receptors were observed in NMDARE microbiota recipient mice following immunization. Overall, our findings demonstrated that intestinal dysbiosis increased NMDARE susceptibility, suggesting a new target for limiting the occurrence of the severe phenotype of NMDARE.}, }
@article {pmid38030004, year = {2023}, author = {Liu, Y and Deng, G and Liu, H and Chen, P and Pan, Y and Chen, L and Chen, H and Zhang, G}, title = {Seasonal variations of airborne microbial diversity in waste transfer stations and preventive effect on Streptococcus pneumoniae induced pulmonary inflammation.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {168888}, doi = {10.1016/j.scitotenv.2023.168888}, pmid = {38030004}, issn = {1879-1026}, abstract = {Environment, location, and season are important factors that influence the microbiological community, yet, little research on airborne microorganisms in waste transfer stations (WTSs). Here, the airborne bacterial and fungal communities at four WTSs during different seasons were analyzed by high-throughput sequencing. The bacteria were isolated by cultural method and screened bacterium alleviate inflammation induced by Streptococcus pneumoniae (Spn) by regulating gut microbiome. The results revealed that collected bioaerosols from the WTSs varied significantly by location and season. Proteobacteria and Pseudomonadota are prevalent in summer and winter, respectively. Ascomycota was predominant in two seasons. Hazard quotients for adults from four WTSs were below one. Three selected potential probiotics were formulated into a microbial preparation with a carrier that effectively prevented inflammation in bacterial and animal experiments. The expression levels of interleukin-1β, interleukin-6, and tumor necrosis factor-α in Pre group (0.11, 0.17, and 0.48-fold) were significantly lower than Spn group (2.75, 1.71, and 5.01-fold). These mechanisms are associated with changes in gut microbiota composition and short-chain fatty acids (SCFAs) levels, such as affecting Lachnospiraceae lachnospira abundance and acetic acid content. This study provides insights into the potential application of probiotics derived from WTSs as an alternative approach to preventing respiratory infections.}, }
@article {pmid38029942, year = {2023}, author = {Xie, Z and Zhou, J and Zhang, X and Li, Z}, title = {Clinical potential of microbiota in thyroid cancer therapy.}, journal = {Biochimica et biophysica acta. Molecular basis of disease}, volume = {1870}, number = {2}, pages = {166971}, doi = {10.1016/j.bbadis.2023.166971}, pmid = {38029942}, issn = {1879-260X}, abstract = {Thyroid cancer is one of the most common tumors of the endocrine system because of its rapid and steady increase in incidence and prevalence. In recent years, a growing number of studies have identified a key role for the gut, thyroid tissue and oral microbiota in the regulation of metabolism and the immune system. A growing body of evidence has conclusively demonstrated that the microbiota influences tumor formation, prevention, diagnosis, and treatment. We provide extensive information in which oral, gut, and thyroid microbiota have an effect on thyroid cancer development in this review. In addition, we thoroughly discuss the various microbiota species, their potential functions, and the underlying mechanisms for thyroid cancer. The microbiome offers a unique opportunity to improve the effectiveness of immunotherapy and radioiodine therapy thyroid cancer by maintaining the right type of microbiota, and holds great promise for improving clinical outcomes and quality of life for thyroid cancer patients.}, }
@article {pmid38029921, year = {2023}, author = {Lian, V and Hinrichs, H and Young, M and Faerber, A and Özler, O and Xie, Y and Ballentine, SJ and Tarr, PI and Davidson, NO and Thompson, MD}, title = {MATERNAL OBESOGENIC DIET ATTENUATES MICROBIOME DEPENDENT OFFSPRING WEANING REACTION WITH WORSENING OF STEATOTIC LIVER DISEASE.}, journal = {The American journal of pathology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajpath.2023.11.006}, pmid = {38029921}, issn = {1525-2191}, abstract = {The mechanisms by which maternal obesity increases the susceptibility to steatotic liver disease (SLD) in offspring are incompletely understood and models using different maternal obesogenic diets (MODEs) display phenotypic variability, likely reflecting the influence of timing and diet composition. Here we compare three maternal obesogenic diets using standardized exposure times to identify differences in offspring disease progression. We found that the severity of hepatic inflammation and fibrosis in offspring depends on the composition of maternal obesogenic diet. Offspring cecal microbiome composition was shifted in all MODE groups relative to control. Decreased alpha-diversity in some MODE offspring with shifts in abundance of multiple genera suggestive of delayed maturation of the microbiome. Next we demonstrated that the weaning reaction typically characterized by a spike in intestinal expression of Tnfa and Ifng is attenuated in MODE offspring in an early microbiome dependent manner shown using cross-fostering. Cross-fostering also switched the severity of disease progression in offspring dependent on the diet of the fostering dam. These results identify maternal diet composition and timing of exposure as modifiers in mediating transmissible changes in the microbiome. These changes in the early microbiome alter a critical window during weaning that drives susceptibility to progressive liver disease in offspring.}, }
@article {pmid38029741, year = {2023}, author = {Meyer, KM and Muscettola, IE and Vasconcelos, ALS and Sherman, JK and Metcalf, CJE and Lindow, SE and Koskella, B}, title = {Conspecific versus heterospecific transmission shapes host specialization of the phyllosphere microbiome.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2023.11.002}, pmid = {38029741}, issn = {1934-6069}, abstract = {In disease ecology, pathogen transmission among conspecific versus heterospecific hosts is known to shape pathogen specialization and virulence, but we do not yet know if similar effects occur at the microbiome level. We tested this idea by experimentally passaging leaf-associated microbiomes either within conspecific or across heterospecific plant hosts. Although conspecific transmission results in persistent host-filtering effects and more within-microbiome network connections, heterospecific transmission results in weaker host-filtering effects but higher levels of interconnectivity. When transplanted onto novel plants, heterospecific lines are less differentiated by host species than conspecific lines, suggesting a shift toward microbiome generalism. Finally, conspecific lines from tomato exhibit a competitive advantage on tomato hosts against those passaged on bean or pepper, suggesting microbiome-level host specialization. Overall, we find that transmission mode and previous host history shape microbiome diversity, with repeated conspecific transmission driving microbiome specialization and repeated heterospecific transmission promoting microbiome generalism.}, }
@article {pmid38029703, year = {2023}, author = {Liu, H and Feng, X and Wang, D and Liu, L and Liu, Y and Liu, B and Zhu, L and Zhang, C and Yang, W}, title = {Altered metabolome and microbiome features provide clues in predicting recurrence of ulcerative colitis.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {239}, number = {}, pages = {115864}, doi = {10.1016/j.jpba.2023.115864}, pmid = {38029703}, issn = {1873-264X}, abstract = {PURPOSE: Many studies have shown that the imbalance of the intestinal flora and metabolite can lead to the development of ulcerative colitis (UC), but their role in recurrent-UC is still unclear. We studied the intestinal flora and metabolites associated with recurrent-UC to elucidate the mechanism and biomarkers of recurrent-UC.<br><br>METHODS: Ulcerative colitis (UC) models in active, remission, and recurrence stages were established, and the abundance of intestinal flora was determined by 16&#xa0;S rRNA sequencing. The changes in the metabolites present in feces and serum were analyzed by UPLC-MS/MS.<br><br>RESULTS: We identified 24 metabolites in feces and serum, which might be used as diagnostic and predictive biomarkers of recurrent-UC. The dominant flora of recurrent-UC included Romboutsia, UCG-005, etc. The results of a network analysis found that long-chain fatty acids and phenylalanine were strongly correlated with Firmicutes and Proteobacteria, which indicated that the recurrence of UC might be closely related to metabolites and microorganisms.<br><br>CONCLUSION: The changes in intestinal microbiota and metabolites are closely related to the development of UC. Microbiota is an important inducer of UC, which can regulate metabolites through the 'microorganism-gut-metabolite' axis. It may provide a new method for the prediction and treatment of UC.}, }
@article {pmid38029586, year = {2023}, author = {Fan, Y and Keerthisinghe, TP and Nian, M and Cao, X and Chen, X and Yang, Q and Sampathkumar, K and Loo, JSC and Ng, KW and Demokritou, P and Fang, M}, title = {Comparative secretome metabolic dysregulation by six engineered dietary nanoparticles (EDNs) on the simulated gut microbiota.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133003}, doi = {10.1016/j.jhazmat.2023.133003}, pmid = {38029586}, issn = {1873-3336}, abstract = {The potential use of engineered dietary nanoparticles (EDNs) in diet has been increasing and poses a risk of exposure. The effect of EDNs on gut bacterial metabolism remains largely unknown. In this study, liquid chromatography-mass spectrometry (LC-MS) based metabolomics was used to reveal significantly altered metabolites and metabolic pathways in the secretome of simulated gut microbiome exposed to six different types of EDNs (Chitosan, cellulose nanocrystals (CNC), cellulose nanofibrils (CNF) and polylactic-co-glycolic acid (PLGA); two inorganic EDNs including TiO2 and SiO2) at two dietary doses. We demonstrated that all six EDNs can alter the composition in the secretome with distinct patterns. Chitosan, followed by PLGA and SiO2, has shown the highest potency in inducing the secretome change with major pathways in tryptophan and indole metabolism, bile acid metabolism, tyrosine and phenol metabolism. Metabolomic alterations with clear dose response were observed in most EDNs. Overall, phenylalanine has been shown as the most sensitive metabolites, followed by bile acids such as chenodeoxycholic acid and cholic acid. Those metabolites might be served as the representative metabolites for the EDNs-gut bacteria interaction. Collectively, our studies have demonstrated the sensitivity and feasibility of using metabolomic signatures to understand and predict EDNs-gut microbiome interaction.}, }
@article {pmid38029543, year = {2023}, author = {Ohkubo, T and Matsumoto, Y and Sasaki, H and Kinoshita, K and Ogasawara, Y and Sugita, T}, title = {Citrobacter koseri inhibits the growth of Staphylococcus epidermidis by suppressing iron utilization.}, journal = {Biochemical and biophysical research communications}, volume = {691}, number = {}, pages = {149277}, doi = {10.1016/j.bbrc.2023.149277}, pmid = {38029543}, issn = {1090-2104}, abstract = {The human skin microbiome consists of many species of bacteria, including Staphylococcus aureus and S. epidermidis. Individuals with atopic dermatitis (AD) have an increased relative abundance of S. aureus, which exacerbates the inflammation of AD. Although S. epidermidis, a main component of healthy skin microbiota, inhibits the growth of S. aureus, the balance between S. epidermidis and S. aureus is disrupted in the skin of individuals with AD. In this study, we found that Citrobacter koseri isolated from patients with AD produces substances that inhibit the growth of S. epidermidis. Heat-treated culture supernatant (CS) of C. koseri inhibited the growth of S. epidermidis but not S. aureus. The genome of C. koseri has gene clusters related to siderophores and the heat-treated CS of C. koseri contained a high concentration of siderophores compared with the control medium. The inhibitory activity of C. koseri CS against the growth of S. epidermidis was decreased by the addition of iron, but not copper or zinc. Deferoxamine, an iron-chelating agent, also inhibited the growth of S. epidermidis, but not that of S. aureus. These findings suggest that C. koseri inhibits the growth of S. epidermidis by interfering with its iron utilization.}, }
@article {pmid38029490, year = {2023}, author = {Thomas, S and Lappin, DF and Bennett, D and Nile, C and Riggio, MP}, title = {Elevated pro-inflammatory cytokines and chemokines in saliva of cats with feline odontoclastic resorptive lesion.}, journal = {Research in veterinary science}, volume = {166}, number = {}, pages = {105092}, doi = {10.1016/j.rvsc.2023.105092}, pmid = {38029490}, issn = {1532-2661}, abstract = {Feline odontoclastic resorptive lesion (FORL) is an inflammatory oral disease of unknown aetiopathogenesis that affects between 20% to 75% of cats. Twenty immune-associated molecules were measured in saliva of 25 healthy and 40 cats with FORL using a multiplex assay. No statistically significant differences were observed in the levels of these proteins between the healthy group and the diseased group of cats. A two-step cluster analysis of the oral microbiome and salivary cytokine data identified two subgroups of cats with FORL: FORL-1 (subset of cats with a less diverse oral microbiome) and FORL-2 (diseased cats with a microbiome similar to that of healthy animals). The level of some key proinflammatory cytokines (IL-1β, IL-12p40) and chemokines (IL-8, RANTES, KC) were significantly higher in the FORL-1 subgroup than in the FORL-2 subgroup and the healthy group. In addition, TNF-α levels were greater in the FORL-1 subgroup than in the FORL-2 subgroup. These increases in pro-inflammatory cytokines and chemokines indicate active ongoing inflammation that may promote the osteoclastic/odontoclastic activity associated with FORL.}, }
@article {pmid38029259, year = {2023}, author = {Ogai, K and Nana, BC and Lloyd, YM and Arios, JP and Jiyarom, B and Awanakam, H and Esemu, LF and Hori, A and Matsuoka, A and Nainu, F and Megnekou, R and Leke, RGF and Ekali, GL and Okamoto, S and Kuraishi, T}, title = {Skin microbiome profile in people living with HIV/AIDS in Cameroon.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1211899}, pmid = {38029259}, issn = {2235-2988}, abstract = {The presence of pathogens and the state of diseases, particularly skin diseases, may alter the composition of human skin microbiome. HIV infection has been reported to impair gut microbiome that leads to severe consequences. However, with cutaneous manifestations, that can be life-threatening, due to the opportunistic pathogens, little is known whether HIV infection might influence the skin microbiome and affect the skin homeostasis. This study catalogued the profile of skin microbiome of healthy Cameroonians, at three different skin sites, and compared them to the HIV-infected individuals. Taking advantage on the use of molecular assay coupled with next-generation sequencing, this study revealed that alpha-diversity of the skin microbiome was higher and beta-diversity was altered significantly in the HIV-infected Cameroonians than in the healthy ones. The relative abundance of skin microbes such as Micrococcus and Kocuria species was higher and Cutibacterium species was significantly lower in HIV-infected people, indicating an early change in the human skin microbiome in response to the HIV infection. This phenotypical shift was not related to the number of CD4 T cell count thus the cause remains to be identified. Overall, these data may offer an important lead on the role of skin microbiome in the determination of cutaneous disease state and the discovery of safe pharmacological preparations to treat microbial-related skin disorders.}, }
@article {pmid38029257, year = {2023}, author = {Liu, H and Hu, Q and Yan, Q and Hao, Z and Liang, C}, title = {Alterations in urinary microbiota composition in urolithiasis patients: insights from 16S rRNA gene sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1266446}, pmid = {38029257}, issn = {2235-2988}, abstract = {OBJECTIVES: To investigate the urinary microbiota composition in urolithiasis patients compared to healthy controls and to identify potential microbial markers and their association with clinical parameters.<br><br>METHODS: A total of 66 samples, comprising 45 from urolithiasis patients and 21 from healthy controls, were analyzed. 16S rRNA gene sequencing was employed to determine the microbiota composition. Various statistical and bioinformatics tools, including ANOVA, PCoA, and LEfSe, were utilized to analyze the sequencing data and identify significant differences in microbial abundance.<br><br>RESULTS: No significant demographic differences were observed between the two groups. Post-quality control, clean tags ranged from 60,979 to 68,736. Significant differences in &#x3b1;-diversity were observed between the two groups. &#x3b2;-diversity analysis revealed distinct clustering of the urinary microbiota in urolithiasis patients and controls. Notably, Ruminococcaceae was predominant in urolithiasis samples, while Proteobacteria was more prevalent in healthy samples. Lactobacillus was significantly overrepresented in samples from healthy females.<br><br>CONCLUSION: The urinary microbiota composition in urolithiasis patients is distinct from that of healthy controls. Specific microbial taxa, such as Ruminococcaceae and Proteobacteria, could serve as potential biomarkers for urolithiasis. The findings pave the way for further exploration of the role of microbiota in urolithiasis and the development of microbiome-based therapeutic strategies.}, }
@article {pmid38029244, year = {2023}, author = {Zong, Y and Wang, X and Wang, J}, title = {Research progress on the correlation between gut microbiota and preeclampsia: microbiome changes, mechanisms and treatments.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1256940}, pmid = {38029244}, issn = {2235-2988}, abstract = {Preeclampsia is a specific disease during pregnancy and is a significant factor in the increased mortality in perinatal women. Gut microbiota, an intricate and abundant microbial community in the digestive tract, is crucial for host metabolism, immunity, and nutrient absorption. The onset and progression of preeclampsia are closely correlated with the changes in maternal gut microbiota. Research purpose was to compile the existing bits of present scientific data and to close the gap in the knowledge of changes in gut microbiota in preeclampsia and their association with preeclampsia. We searched studies from two electronic databases (PubMed and Web of Science) included from 2014 to 2023. This review is divided into three parts. In the first part, the author elaborates longitudinal differences of maternal gut microbiota during different gestation periods. In the second part, we discuss that gut microbiota can lead to the occurrence of preeclampsia by systemic immune response, influencing the release of active peptides, short-chain fatty acids, trimethylamine-N-oxide (TMAO) and other metabolites, vascular factors and Microorganism-immune axis. In the third part, we proposed that a high-fiber diet combined with drugs and microecological regulators may be therapeutic in enhancing or preventing the emergence and evolution of preeclampsia, which needs further exploration. Although the pathogenesis of preeclampsia is still nebulous and there is no clear and valid clinical treatment, our study provides new ideas for the pathogenesis, prevention and treatment of preeclampsia.}, }
@article {pmid38029238, year = {2023}, author = {Nie, Q and Wan, X and Tao, H and Yang, Q and Zhao, X and Liu, H and Hu, J and Luo, Y and Shu, T and Geng, R and Gu, Z and Fan, F and Liu, Z}, title = {Multi-function screening of probiotics to improve oral health and evaluating their efficacy in a rat periodontitis model.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1261189}, pmid = {38029238}, issn = {2235-2988}, abstract = {The oral cavity is the second most microbially rich region of the human body, and many studies have shown that there is a strong association between microorganisms and oral health. Some pathogenic bacteria produce biofilms and harmful metabolites in the mouth that may cause oral problems such as oral malodor, periodontitis, and dental caries. Altering the oral microbiota by using probiotics may alleviate oral health problems. Thus, using multi-function screening, we aimed to identify probiotics that can significantly improve oral health. The main parameters were the inhibition of pathogenic bacteria growth, inhibition of biofilm formation, reduction in the production of indole, H2S, and NH3 metabolites that cause halitosis, increase in the production of H2O2 to combat harmful bacteria, and co-aggregation with pathogens to prevent their adhesion and colonization in the oral cavity. Tolerance to cholic acid and choline was also assessed. Bifidobacterium animalis ZK-77, Lactobacillus salivarius ZK-88, and Streptococcus salivarius ZK-102 had antibacterial activity and inhibited biofilm production to prevent caries. They also improved the oral malodor parameter, H2S, NH3, and indole production. The selected probiotics (especially L. salivarius ZK-88) alleviated the inflammation in the oral cavity of rats with periodontitis. The analysis of the gingival crevicular fluid microbiome after probiotic intervention showed that B. animalis ZK-77 likely helped to restore the oral microbiota and maintain the oral microecology. Next, we determined the best prebiotics for each candidate probiotic in order to obtain a formulation with improved effects. We then verified that a probiotics/prebiotic combination (B. animalis ZK-77, L. salivarius ZK-88, and fructooligosaccharides) significantly improved halitosis and teeth color in cats. Using whole-genome sequencing and acute toxicity mouse experiments involving the two probiotics, we found that neither probiotic had virulence genes and they had no significant effects on the growth or development of mice, indicating their safety. Taking the results together, B. animalis ZK-77 and L. salivarius ZK-88 can improve oral health, as verified by in vivo and in vitro experiments. This study provides a reference for clinical research and also provides new evidence for the oral health benefits of probiotics.}, }
@article {pmid38029215, year = {2023}, author = {Jin, X and Xiao, J and Lu, C and Ma, W and Fan, Y and Xue, X and Xia, Y and Chen, N and Liu, J and Pei, X}, title = {Breastmilk microbiome changes associated with lactational mastitis and treatment with dandelion extract.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1247868}, pmid = {38029215}, issn = {1664-302X}, abstract = {INTRODUCTION: Dandelion (Pugongying) is one of the most frequently used Chinese herbs for treating lactational mastitis (LM). Pugongying granules, a patented medication primarily comprised of dandelion extract, have been approved by CFDA for LM treatment in China. The aims of this study were to investigate the etiology of LM and the mechanism by which Pugongying granules decrease LM symptoms, with a particular focus on the microbial communities found in breastmilk.<br><br>METHODS: Participants were recruited from a previously performed randomized controlled trial (Identifier: NCT03756324, ClinicalTrials.gov). Between 2019 and 2020, women diagnosed with unilateral LM at the Beijing University of Chinese Medicine Third Affiliated Hospital were enrolled. In total, 42 paired breastmilk samples from the healthy and affected breasts of the participants were collected. Additionally, 37 paired pre- and post-treatment breastmilk samples from the affected breast were collected from women who received a 3-day course of either Pugongying granules (20 women) or cefdinir (17 women). Clinical outcomes [e.g., body temperature, visual analogue scale (VAS) score for breast pain, the percentage of neutrophils (NE%)] were analyzed pre- and post-treatment, and the breastmilk samples were subjected to 16S rRNA gene sequencing to analyze the alpha and beta diversities and identify significant bacteria. Finally, the relationship between microorganisms and clinical outcomes was analyzed.<br><br>RESULTS: There was no significant difference in fever and pain between the Pugongying group and cefdinir group. The most prevalent bacterial genera in breastmilk were Streptococcus and Staphylococcus. Compared to healthy breastmilk, microbial diversity was reduced in affected breastmilk, and there was a higher relative abundance of Streptococcus. After Pugongying treatment, there was an increase in microbial diversity with significantly higher abundance of Corynebacterium. A negative correlation was found between Corynebacterium, VAS score, and NE%. Treatment with cefdinir did not affect microbial diversity. Taken together, our results show a correlation between LM and reduced microbial diversity, as well as an increased abundance of Streptococcus in affected breastmilk.<br><br>CONCLUSION: Pugongying granules enhanced microbial diversity in breastmilk samples. Given the substantial variation in individual microbiomes, identifying specific species of Streptococcus and Corynebacterium associated with LM may provide additional insight into LM pathogenesis and treatment.}, }
@article {pmid38029194, year = {2023}, author = {Smith, JC and Varriano, S and Roach, K and Snipes, Z and Dawson, JL and Shealy, J and Dunn, LL and Snyder, WE and Shariat, NW}, title = {Prevalence and molecular characterization of Salmonella isolated from wild birds in fresh produce environments.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1272916}, pmid = {38029194}, issn = {1664-302X}, abstract = {Wild birds pose a difficult food safety risk to manage because they can avoid traditional wildlife mitigation strategies, such as fences. Birds often use agricultural fields and structures as foraging and nesting areas, which can lead to defecation on crops and subsequent transfer of foodborne pathogens. To assess the food safety risk associated with these events, wild bird feces were collected from produce fields across the southeastern United States during the 2021 and 2022 growing seasons. In total 773 fecal samples were collected from 45 farms across Florida, Georgia, South Carolina, and Tennessee, and 2.1% (n = 16) of samples were Salmonella-positive. Importantly, 75% of Salmonella were isolated from moist feces, showing reduced Salmonella viability when feces dry out. 16S microbiome analysis showed that presence of culturable Salmonella in moist feces correlated to a higher proportion of the Enterobacteriaceae family. From the Salmonella-positive samples, 62.5% (10/16) contained multi-serovar Salmonella populations. Overall, 13 serovars were detected, including six most commonly attributed to human illness (Enteriditis, Newport, Typhimurium, Infantis, Saintpaul, and Muenchen). PCR screening identified an additional 59 Salmonella-positive fecal samples, which were distributed across moist (n = 44) and dried feces (n = 15). On-farm point counts and molecular identification from fecal samples identified 57 bird species, including for 10 Salmonella-positive fecal samples. Overall, there was a low prevalence of Salmonella in fecal samples, especially in dried feces, and we found no evidence of Salmonella transmission to proximal foliage or produce. Fecal samples collected in farms close together shared highly related isolates by whole genome sequencing and also had highly similar Salmonella populations with comparable relative frequencies of the same serovars, suggesting the birds acquired Salmonella from a common source.}, }
@article {pmid38029189, year = {2023}, author = {Zhang, X and Luo, X and Tian, L and Yue, P and Li, M and Liu, K and Zhu, D and Huang, C and Shi, Q and Yang, L and Xia, Z and Zhao, J and Ma, Z and Li, J and Leung, JW and Lin, Y and Yuan, J and Meng, W and Li, X and Chen, Y}, title = {The gut microbiome dysbiosis and regulation by fecal microbiota transplantation: umbrella review.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1286429}, pmid = {38029189}, issn = {1664-302X}, abstract = {BACKGROUND: Gut microbiome dysbiosis has been implicated in various gastrointestinal and extra-gastrointestinal diseases, but evidence on the efficacy and safety of fecal microbiota transplantation (FMT) for therapeutic indications remains unclear.<br><br>METHODS: The gutMDisorder database was used to summarize the associations between gut microbiome dysbiosis and diseases. We performed an umbrella review of published meta-analyses to determine the evidence synthesis on the efficacy and safety of FMT in treating various diseases. Our study was registered in PROSPERO (CRD42022301226).<br><br>RESULTS: Gut microbiome dysbiosis was associated with 117 gastrointestinal and extra-gastrointestinal. Colorectal cancer was associated with 92 dysbiosis. Dysbiosis involving Firmicutes (phylum) was associated with 34 diseases. We identified 62 published meta-analyses of FMT. FMT was found to be effective for 13 diseases, with a 95.56% cure rate (95% CI: 93.88-97.05%) for recurrent Chloridoids difficile infection (rCDI). Evidence was high quality for rCDI and moderate to high quality for ulcerative colitis and Crohn's disease but low to very low quality for other diseases.<br><br>CONCLUSION: Gut microbiome dysbiosis may be implicated in numerous diseases. Substantial evidence suggests FMT improves clinical outcomes for certain indications, but evidence quality varies greatly depending on the specific indication, route of administration, frequency of instillation, fecal preparation, and donor type. This variability should inform clinical, policy, and implementation decisions regarding FMT.}, }
@article {pmid38029184, year = {2023}, author = {Ye, L and Zhang, B and Zhang, L and Yang, X and Tan, W and Zhang, X and Li, X}, title = {Pathogenic invasive microbes Trichoderma pleuroticola transform bacterial and fungal community diversity in Auricularia cornea crop production system.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1263982}, pmid = {38029184}, issn = {1664-302X}, abstract = {Pathogenic invasion of Trichoderma pleuroticola profoundly altered microflora in the Auricularia cornea crop production system, impacting diversity and composition in both artificial bed-log and fruiting bodies. A more complex ecological network between the diseased and healthy bodies. Researchers still have poor knowledge about how the important agricultural relationship between the composition of the microbiome of the artificial bed-log and the fruiting bodies is infected by the pathogenic invasive microbes T. pleuroticola, but this knowledge is crucial if we want to use or improve it. Here, we investigated 8 groups (48 biological samples) across 5 growth stages of the A. cornea production system using metagenomic technology. Diseased and healthy fruiting bodies exhibited distinct microbial compositions, while core members in artificial bed-logs remained stable. Core microbiota analysis highlighted Pseudomonas and Pandoraea bacterial genera, as well as Sarocladium, Cephalotrichum, Aspergillus, and Mortierella fungal genera as biomarker species after the bodies were treated with the pathogenic invasive microbes T. pleuroticola. In diseased bodies, these core members upregulated pathways including polymyxin resistance, L-arginine degradation II, superpathway of L-arginine and L-ornithine degradation, glucose degradation (oxidative), glucose and glucose-1-phosphate degradation, promoting fruit spoilage. Our data confirm that T. pleuroticola plays an important role in the early stages of disease development in the A. cornea crop generation system. The exposed volatile core microbiome may play an important role in accelerating T. pleuroticola-induced decay of fruiting bodies.}, }
@article {pmid38029177, year = {2023}, author = {Rempfert, KR and Kraus, EA and Nothaft, DB and Dildar, N and Spear, JR and Sepúlveda, J and Templeton, AS}, title = {Intact polar lipidome and membrane adaptations of microbial communities inhabiting serpentinite-hosted fluids.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1198786}, pmid = {38029177}, issn = {1664-302X}, abstract = {The generation of hydrogen and reduced carbon compounds during serpentinization provides sustained energy for microorganisms on Earth, and possibly on other extraterrestrial bodies (e.g., Mars, icy satellites). However, the geochemical conditions that arise from water-rock reaction also challenge the known limits of microbial physiology, such as hyperalkaline pH, limited electron acceptors and inorganic carbon. Because cell membranes act as a primary barrier between a cell and its environment, lipids are a vital component in microbial acclimation to challenging physicochemical conditions. To probe the diversity of cell membrane lipids produced in serpentinizing settings and identify membrane adaptations to this environment, we conducted the first comprehensive intact polar lipid (IPL) biomarker survey of microbial communities inhabiting the subsurface at a terrestrial site of serpentinization. We used an expansive, custom environmental lipid database that expands the application of targeted and untargeted lipodomics in the study of microbial and biogeochemical processes. IPLs extracted from serpentinite-hosted fluid communities were comprised of >90% isoprenoidal and non-isoprenoidal diether glycolipids likely produced by archaeal methanogens and sulfate-reducing bacteria. Phospholipids only constituted ~1% of the intact polar lipidome. In addition to abundant diether glycolipids, betaine and trimethylated-ornithine aminolipids and glycosphingolipids were also detected, indicating pervasive membrane modifications in response to phosphate limitation. The carbon oxidation state of IPL backbones was positively correlated with the reduction potential of fluids, which may signify an energy conservation strategy for lipid synthesis. Together, these data suggest microorganisms inhabiting serpentinites possess a unique combination of membrane adaptations that allow for their survival in polyextreme environments. The persistence of IPLs in fluids beyond the presence of their source organisms, as indicated by 16S rRNA genes and transcripts, is promising for the detection of extinct life in serpentinizing settings through lipid biomarker signatures. These data contribute new insights into the complexity of lipid structures generated in actively serpentinizing environments and provide valuable context to aid in the reconstruction of past microbial activity from fossil lipid records of terrestrial serpentinites and the search for biosignatures elsewhere in our solar system.}, }
@article {pmid38029176, year = {2023}, author = {Jain, U and Poltronieri, P and Fusco, V and Primiceri, E}, title = {Editorial: Latest perspective on microbes detection: from laboratory to on-spot sensor.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1302805}, doi = {10.3389/fmicb.2023.1302805}, pmid = {38029176}, issn = {1664-302X}, }
@article {pmid38029169, year = {2023}, author = {Nguyen, TQ and Martínez-Álvaro, M and Lima, J and Auffret, MD and Rutherford, KMD and Simm, G and Dewhurst, RJ and Baima, ET and Roehe, R}, title = {Identification of intestinal and fecal microbial biomarkers using a porcine social stress model.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1197371}, pmid = {38029169}, issn = {1664-302X}, abstract = {Understanding the relationships between social stress and the gastrointestinal microbiota, and how they influence host health and performance is expected to have many scientific and commercial implementations in different species, including identification and improvement of challenges to animal welfare and health. In particular, the study of the stress impact on the gastrointestinal microbiota of pigs may be of interest as a model for human health. A porcine stress model based on repeated regrouping and reduced space allowance during the last 4 weeks of the finishing period was developed to identify stress-induced changes in the gut microbiome composition. The application of the porcine stress model resulted in a significant increase in salivary cortisol concentration over the course of the trial and decreased growth performance and appetite. The applied social stress resulted in 32 bacteria being either enriched (13) or depleted (19) in the intestine and feces. Fecal samples showed a greater number of microbial genera influenced by stress than caecum or colon samples. Our trial revealed that the opportunistic pathogens Treponema and Clostridium were enriched in colonic and fecal samples from stressed pigs. Additionally, genera such as Streptococcus, Parabacteroides, Desulfovibrio, Terrisporobacter, Marvinbryantia, and Romboutsia were found to be enriched in response to social stress. In contrast, the genera Prevotella, Faecalibacterium, Butyricicoccus, Dialister, Alloprevotella, Megasphaera, and Mitsuokella were depleted. These depleted bacteria are of great interest because they synthesize metabolites [e.g., short-chain fatty acids (SCFA), in particular, butyrate] showing beneficial health benefits due to inhibitory effects on pathogenic bacteria in different animal species. Of particular interest are Dialister and Faecalibacterium, as their depletion was identified in a human study to be associated with inferior quality of life and depression. We also revealed that some pigs were more susceptible to pathogens as indicated by large enrichments of opportunistic pathogens of Clostridium, Treponema, Streptococcus and Campylobacter. Generally, our results provide further evidence for the microbiota-gut-brain axis as indicated by an increase in cortisol concentration due to social stress regulated by the hypothalamic-pituitary-adrenal axis, and a change in microbiota composition, particularly of bacteria known to be associated with pathogenicity and mental health diseases.}, }
@article {pmid38029159, year = {2023}, author = {Huang, B and Khan, MZ and Chen, Y and Liang, H and Kou, X and Wang, X and Ren, W and Wang, C and Zhang, Z}, title = {Yeast polysaccharide supplementation: impact on lactation, growth, immunity, and gut microbiota in Dezhou donkeys.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1289371}, pmid = {38029159}, issn = {1664-302X}, abstract = {INTRODUCTION: The Dezhou donkey, a prominent Chinese breed, is known for its remarkable size, rapid growth, and resilience to tough feeding conditions, and disease resistance. These traits are crucial in meeting the growing demand for Ejiao and donkey meat. Yeast polysaccharide (YPS), a functional polysaccharide complex known for its immune-enhancing and growth-promoting properties in livestock and poultry, remains relatively understudied in donkeys.<br><br>OBJECTIVES: This study aimed to investigate the impact of YPS supplementation on lactating and growing Dezhou donkey jennies and foals.<br><br>MATERIALS AND METHODS: Twelve 45-day-old Dezhou donkey foals and their jennies, matched for body weight and age, were randomly allocated to two dietary groups: a control group receiving a basal diet and an experimental group receiving the basal diet supplemented with 10&#x2009;g/pen of YPS. The experiment was conducted over a 23-day period, during which donkey foals and lactating jennies were co-housed.<br><br>RESULTS AND DISCUSSION: The findings revealed that YPS supplementation had no adverse effects on milk production or composition in Dezhou donkey jennies but significantly increased feed intake. Additionally, YPS was associated with increased plasma glucose and creatinine concentrations in foals, while tending to decrease alkaline phosphatase, white blood cell count, red blood cell count, and hemoglobin levels (p&#x2009;<&#x2009;0.10). Immune indices demonstrated that YPS supplementation elevated the levels of immunoglobulin A (IgA) and immunoglobulin G (IgG) in jennies (p&#x2009;<&#x2009;0.05) and increased complement component C4 concentrations in foals (p&#x2009;<&#x2009;0.05). Moreover, YPS positively influenced the fecal microbiome, promoting the abundance of beneficial microorganisms such as Lactobacillus and Prevotella in donkey foals and Terriporobacter and Cellulosilyticum in jennies, all of which contribute to enhanced feed digestion. Additionally, YPS induced alterations in the plasma metabolome for both jennies and foals, with a predominant presence of lipids and lipid-like molecules. Notably, YPS increased the concentrations of specific lipid metabolites, including 13,14-Dihydro PGF2a, 2-Isopropylmalic acid, 2,3-Dinor-TXB2, Triterpenoids, Taurocholic acid, and 3b-Allotetrahydrocortisol, all of which are associated with improved animal growth.<br><br>CONCLUSION: In conclusion, this study suggests that dietary supplementation of YPS enhances feed intake, boosts immunity by increasing immunoglobulin levels, stimulates the growth-promoting gut microbiota (Lactobacillus and Prevotella), and exerts no adverse effects on the metabolism of both Dezhou donkey jennies and foals.}, }
@article {pmid38029157, year = {2023}, author = {Liu, M and Ding, J and Lu, M}, title = {Influence of symbiotic bacteria on the susceptibility of Plagiodera versicolora to Beauveria bassiana infection.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1290925}, pmid = {38029157}, issn = {1664-302X}, abstract = {The symbiotic bacterial microbiota of insects has been shown to play essential roles in processes related to physiology, metabolism, and innate immunity. In this study, the symbiotic microbiome of Plagiodera versicolora at different developmental stages was analyzed using 16S rRNA high-throughput sequencing. The result showed that symbiotic bacteria community in P. versicolora was primarily made up of Actinobacteriota, Proteobacteria, Firmicutes, Bacteroidota, and Dependentiae. The bacterial composition among different age individuals were highly diverse, while 65 core genera were distributed in all samples which recommend core bacterial microbiome. The 8 species core bacteria were isolated from all samples, and all of them were classified as Pseudomonas sp. Among them, five species have been proven to promote the vegetable growth of Beauveria bassiana. Moreover, the virulence of B. bassiana against nonaxenic larvae exceeded B. bassiana against axenic larvae, and the introduction of the Pseudomonas sp. to axenic larvae augmented the virulence of fungi. Taken together, our study demonstrates that the symbiotic bacteria of P. versicolora are highly dissimilar, and Pseudomonas sp. core bacteria can promote host infection by entomopathogenic fungus. This result emphasizes the potential for harnessing these findings in the development of effective pest management strategies.}, }
@article {pmid38029153, year = {2023}, author = {Wu, C and Lower, BA and Moreira, R and Dorantes, D and Le, T and Giurgiu, C and Shi, Y and van der Donk, WA}, title = {Investigation into the mechanism of action of the antimicrobial peptide epilancin 15X.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1247222}, pmid = {38029153}, issn = {1664-302X}, abstract = {Addressing the current antibiotic-resistance challenge would be aided by the identification of compounds with novel mechanisms of action. Epilancin 15X, a lantibiotic produced by Staphylococcus epidermidis 15 × 154, displays antimicrobial activity in the submicromolar range against a subset of pathogenic Gram-positive bacteria. S. epidermidis is a common member of the human skin or mucosal microbiota. We here investigated the mechanism of action of epilancin 15X. The compound is bactericidal against Staphylococcus carnosus as well as Bacillus subtilis and appears to kill these bacteria by membrane disruption. Structure-activity relationship studies using engineered analogs show that its conserved positively charged residues and dehydroamino acids are important for bioactivity, but the N-terminal lactyl group is tolerant of changes. Epilancin 15X treatment negatively affects fatty acid synthesis, RNA translation, and DNA replication and transcription without affecting cell wall biosynthesis. The compound appears localized to the surface of bacteria and is most potent in disrupting the membranes of liposomes composed of negatively charged membrane lipids in a lipid II independent manner. Epilancin 15X does not elicit a LiaRS response in B. subtilis but did upregulate VraRS in S. carnosus. Treatment of S. carnosus or B. subtilis with epilancin 15X resulted in an aggregation phenotype in microscopy experiments. Collectively these studies provide new information on epilancin 15X activity.}, }
@article {pmid38029152, year = {2023}, author = {Huang, Z and He, X and Zhang, C and Zhang, M and Wang, J and Hou, Y and Wang, D and Yao, S and Yu, Q and Ji, K}, title = {Microbial communities and functions changed in rhizosphere soil of Pinus massoniana provenances with different carbon storage.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1264670}, pmid = {38029152}, issn = {1664-302X}, abstract = {INTRODUCTION: The average carbon storage of Pinus massoniana is much higher than the average carbon storage of Chinese forests, an important carbon sink tree species in subtropical regions of China. However, there are few studies on the differences in rhizosphere microorganisms of P. massoniana with different carbon storages.<br><br>METHODS: To clarify the relationships between plant carbon storage level, environmental parameters and microbial community structure, we identified three carbon storage levels from different P. massoniana provenances and collected rhizosphere soil samples. We determined chemical properties of soil, extracellular enzyme activity, and microbial community structures at different carbon storage levels and examined how soil factors affect rhizosphere microorganisms under different carbon storage levels.<br><br>RESULTS: The results revealed that soil organic carbon (SOC), nitrate nitrogen (NO3[-]-N), ammonium nitrogen (NH4[+]-N) contents all increased with increasing carbon storage levels, while pH decreased accordingly. In contrast, the available phosphorus (AP) content did not change significantly. The soil AP content was within the range of 0.91&#x2009;~&#x2009;1.04&#x2009;mg/kg. The microbial community structure of P. massoniana changed with different carbon storage, with Acidobacteria (44.27%), Proteobacteria (32.57%), and Actinobacteria (13.43%) being the dominant bacterial phyla and Basidiomycota (73.36%) and Ascomycota (24.64%) being the dominant fungal phyla across the three carbon storage levels. Soil fungi were more responsive to carbon storage than bacteria in P. massoniana. C/N, NH4[+]-N, NO3[-]-N, and SOC were the main drivers (p&#x2009;<&#x2009;0.05) of changes in rhizosphere microbial communities.<br><br>DISCUSSION: The results revealed that in the rhizosphere there were significant differences in soil carbon cycle and microorganism nutrient preferences at different carbon storages of P. massoniana provenance, which were significantly related to the changes in rhizosphere microbial community structure. Jiangxi Anyuan (AY) provenance is more suitable for the construction of high carbon storage plantation.}, }
@article {pmid38029138, year = {2023}, author = {Portugal, A and Liu, X and Pyzik, A and Trovão, J}, title = {Editorial: Microbiomes of art and their importance in preserving cultural heritage.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1321133}, doi = {10.3389/fmicb.2023.1321133}, pmid = {38029138}, issn = {1664-302X}, }
@article {pmid38029137, year = {2023}, author = {Qian, X and Fu, Z and Diao, C and Zhang, W and Tao, W and Hu, J and Zhang, S and Zhao, D}, title = {Genetic causal relationship between gut microbiome and psoriatic arthritis: a bidirectional two-sample Mendelian randomization study.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1265786}, pmid = {38029137}, issn = {1664-302X}, abstract = {BACKGROUND: Several observational studies have suggested a potential relationship between gut microbiome and psoriatic arthritis (PsA). However, the causality of this relationship still remains unclear. We aim to explore if the specific gut microbiome is causally associated with PsA at the genetic level and offer valuable insights into the etiology of PsA.<br><br>METHODS: In this study, we employed a bidirectional two-sample Mendelian randomization (MR) analysis to investigate the causal effects of the gut microbiome on PsA. Publicly accessible genome-wide association study summary data of gut microbiome were obtained from the MiBioGen consortium (n&#x2009;=&#x2009;14,306), while the summary statistics of psoriatic arthropathies were sourced from the FinnGen consortium R8 release data (2,776 cases and 221,323 controls). The primary analytical method employed was inverse variance weighted (IVW), complemented by supplementary methods including MR-Egger, weighted median, weighted mode, maximum likelihood, MR-PRESSO, and cML-MA. Reverse MR analysis was performed on the bacteria that were found to be causally associated with PsA in forward MR analysis. Cochran's IVW Q statistic was utilized to assess the heterogeneity of instrumental variables among the selected single nucleotide polymorphisms.<br><br>RESULTS: IVW estimates revealed that Ruminococcaceae_UCG-002 (odds ratio (OR)&#x2009;=&#x2009;0.792, 95% confidence interval (CI), 0.643-0.977, p =&#x2009;0.029) exhibited a protective effect on PsA. Conversely, Blautia (OR&#x2009;=&#x2009;1.362, 95% CI, 1.008-1.842, p =&#x2009;0.044), Eubacterium_fissicatena_group (OR&#x2009;=&#x2009;1.28, 95% CI, 1.075-1.524, p =&#x2009;0.006), and Methanobrevibacter (OR&#x2009;=&#x2009;1.31, 95% CI, 1.059-1.621, p =&#x2009;0.013) showed a positive correlation with the risk of PsA. No significant heterogeneity, horizontal pleiotropy, or outliers were observed, and the results of the MR analysis remained unaffected by any single nucleotide polymorphisms. According to the results of reverse MR analysis, no significant causal effect of PsA was found on gut microbiome.<br><br>CONCLUSION: This study establishes for the first time a causal relationship between the gut microbiome and PsA, providing potential valuable strategies for the prevention and treatment of PsA. Further randomized controlled trials are urgently warranted to support the targeted protective mechanisms of probiotics on PsA.}, }
@article {pmid38029135, year = {2023}, author = {Maingi, FM and Akutse, KS and Ajene, IJ and Omolo, KM and Khamis, FM}, title = {Immunological responses and gut microbial shifts in Phthorimaea absoluta exposed to Metarhizium anisopliae isolates under different temperature regimes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1258662}, pmid = {38029135}, issn = {1664-302X}, abstract = {The invasive tomato leaf miner, Phthorimaea absoluta, is conventionally controlled through chemical insecticides. However, the rise of insecticide resistance has necessitated sustainable and eco-friendly alternatives. Entomopathogenic fungi (EPF) have shown potential due to their ability to overcome resistance and have minimal impact on non-target organisms. Despite this potential, the precise physiological mechanisms by which EPF acts on insect pests remain poorly understood. To attain a comprehensive understanding of the complex physiological processes that drive the successful control of P. absoluta adults through EPF, we investigated the impacts of different Metarhizium anisopliae isolates (ICIPE 665, ICIPE 20, ICIPE 18) on the pest's survival, cellular immune responses, and gut microbiota under varying temperatures. The study unveiled that ICIPE 18 caused the highest mortality rate among P. absoluta moths, while ICIPE 20 exhibited the highest significant reduction in total hemocyte counts after 10 days at 25°C. Moreover, both isolates elicited notable shifts in P. absoluta's gut microbiota. Our findings revealed that ICIPE 18 and ICIPE 20 compromised the pest's defense and physiological functions, demonstrating their potential as biocontrol agents against P. absoluta in tomato production systems.}, }
@article {pmid38029134, year = {2023}, author = {Lartey, I and Benucci, GMN and Marsh, TL and Bonito, GM and Melakeberhan, H}, title = {Characterizing microbial communities associated with northern root-knot nematode (Meloidogyne hapla) occurrence and soil health.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1267008}, pmid = {38029134}, issn = {1664-302X}, abstract = {The northern root-knot nematode (Meloidogyne hapla) causes extensive damage to agricultural crops globally. In addition, M. hapla populations with no known genetic or morphological differences exhibit parasitic variability (PV) or reproductive potential based on soil type. However, why M. hapla populations from mineral soil with degraded soil health conditions have a higher PV than populations from muck soil is unknown. To improve our understanding of soil bio-physicochemical conditions in the environment where M. hapla populations exhibited PV, this study characterized the soil microbial community and core- and indicator-species structure associated with M. hapla occurrence and soil health conditions in 15 Michigan mineral and muck vegetable production fields. Bacterial and fungal communities in soils from where nematodes were isolated were characterized with high throughput sequencing of 16S and internal transcribed spacer (ITS) rDNA. Our results showed that M. hapla-infested, as well as disturbed and degraded muck fields, had lower bacterial diversity (observed richness and Shannon) compared to corresponding mineral soil fields or non-infested mineral fields. Bacterial and fungal community abundance varied by soil group, soil health conditions, and/or M. hapla occurrence. A core microbial community was found to consist of 39 bacterial and 44 fungal sub-operational taxonomic units (OTUs) across all fields. In addition, 25 bacteria were resolved as indicator OTUs associated with M. hapla presence or absence, and 1,065 bacteria as indicator OTUs associated with soil health conditions. Out of the 1,065 bacterial OTUs, 73.9% indicated stable soil health, 8.4% disturbed, and 0.4% degraded condition; no indicators were common to the three categories. Collectively, these results provide a foundation for an in-depth understanding of the environment where M. hapla exists and conditions associated with parasitic variability.}, }
@article {pmid38029126, year = {2023}, author = {Shah, T and Hou, Y and Jiang, J and Shah, Z and Wang, Y and Li, Q and Xu, X and Wang, Y and Wang, B and Xia, X}, title = {Comparative analysis of the intestinal microbiome in Rattus norvegicus from different geographies.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1283453}, pmid = {38029126}, issn = {1664-302X}, abstract = {Rat species Rattus norvegicus, also known as the brown street rat, is the most abundant mammal after humans in urban areas, where they co-exist with humans and domestic animals. The reservoir role of R. norvegicus of zoonotic pathogens in cities among rodent-borne diseases that could endanger the lives of humans and other mammals. Therefore, understanding the normal microbiome of R. norvegicus is crucial for understanding and preventing zoonotic pathogen transmission to humans and animals. We investigated the intestinal microbiome of free-living R. norvegicus collected from the Ruili, Nujiang, and Lianhe regions of Yunnan, China, using 16S rRNA gene sequence analysis. Proteobacteria, followed by Firmicutes, and Bacteroidetes were abundant in the intestines of R. norvegicus; however, bacterial compositions varied significantly between samples from different locations. Following a similar trend, Gammaproteobacteria, Bacilli, and Clostridia were among the top bacterial classes in most intestinal samples. The situation differed slightly for the Lianhe and Nujiang samples, although Phyla Bacteroidota and Spirochaetota were most prevalent. The Alpha diversity, Chao1, and Simpson indexes revealed microbial richness among the R. norvegicus samples. A slight variation was observed among the samples collected from Ruili, Nujiang, and Lianhe. At species levels, several opportunistic and zoonotic bacterial pathogens, including Lactococcus garvieae, Uruburuella suis, Bartonella australis, Clostridium perfringens, Streptococcus azizii, Vibrio vulnificus, etc., were revealed in the R. norvegicus intestines, implying the need for a regular survey to monitor and control rodent populations. In conclusion, we explored diverse microbial communities in R. norvegicus intestines captured from different regions. Further, we identified several opportunistic and potential bacterial pathogens, which still need to be tested for their underlying pathogenesis. The findings of our current study should be considered a warning to the health authorities to implement rat control and surveillance strategies globally.}, }
@article {pmid38029121, year = {2023}, author = {Alvarado-Peña, N and Galeana-Cadena, D and Gómez-García, IA and Mainero, XS and Silva-Herzog, E}, title = {The microbiome and the gut-lung axis in tuberculosis: interplay in the course of disease and treatment.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1237998}, pmid = {38029121}, issn = {1664-302X}, abstract = {Tuberculosis is a chronic infectious disease caused by Mycobacterium tuberculosis (MTB) that remains a significant global health challenge. The extensive use of antibiotics in tuberculosis treatment, disrupts the delicate balance of the microbiota in various organs, including the gastrointestinal and respiratory systems. This gut-lung axis involves dynamic interactions among immune cells, microbiota, and signaling molecules from both organs. The alterations of the microbiome resulting from anti-TB treatment can significantly influence the course of tuberculosis, impacting aspects such as complete healing, reinfection, and relapse. This review aims to provide a comprehensive understanding of the gut-lung axis in the context of tuberculosis, with a specific focus on the impact of anti-TB treatment on the microbiome.}, }
@article {pmid38029119, year = {2023}, author = {Moore, GG and Chalivendra, S and Mack, BM and Gilbert, MK and Cary, JW and Rajasekaran, K}, title = {Microbiota of maize kernels as influenced by Aspergillus flavus infection in susceptible and resistant inbreds.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1291284}, pmid = {38029119}, issn = {1664-302X}, abstract = {BACKGROUND: Nearly everything on Earth harbors a microbiome. A microbiome is a community of microbes (bacteria, fungi, and viruses) with potential to form complex networks that involve mutualistic and antagonistic interactions. Resident microbiota on/in an organism are determined by the external environment, both biotic and abiotic, and the intrinsic adaptability of each organism. Although the maize microbiome has been characterized, community changes that result from the application of fungal biocontrol strains, such as non-aflatoxigenic Aspergillus flavus, have not.<br><br>METHODS: We silk channel inoculated field-grown maize separately with a non-aflatoxigenic biocontrol strain (K49), a highly toxigenic strain (Tox4), and a combination of both A. flavus strains. Two maize inbreds were treated, A. flavus-susceptible B73 and A. flavus-resistant CML322. We then assessed the impacts of A. flavus introduction on the epibiota and endobiota of their maize kernels.<br><br>RESULTS: We found that the native microbial communities were significantly affected, irrespective of genotype or sampled tissue. Overall, bacteriomes exhibited greater diversity of genera than mycobiomes. The abundance of certain genera was unchanged by treatment, including genera of bacteria (e.g., Enterobacter, Pantoea) and fungi (e.g., Sarocladium, Meyerozyma) that are known to be beneficial, antagonistic, or both on plant growth and health.<br><br>CONCLUSION: Beneficial microbes like Sarocladium that responded well to A. flavus biocontrol strains are expected to enhance biocontrol efficacy, while also displacing/antagonizing harmful microbes.}, }
@article {pmid38029106, year = {2023}, author = {Ying, ZH and Mao, CL and Xie, W and Yu, CH}, title = {Postbiotics in rheumatoid arthritis: emerging mechanisms and intervention perspectives.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1290015}, pmid = {38029106}, issn = {1664-302X}, abstract = {Rheumatoid arthritis (RA) is a prevalent chronic autoimmune disease that affects individuals of all age groups. Recently, the association between RA and the gut microbiome has led to the investigation of postbiotics as potential therapeutic strategies. Postbiotics refer to inactivated microbial cells, cellular components, or their metabolites that are specifically intended for the microbiota. Postbiotics not only profoundly influence the occurrence and development of RA, but they also mediate various inflammatory pathways, immune processes, and bone metabolism. Although they offer a variety of mechanisms and may even be superior to more conventional "biotics" such as probiotics and prebiotics, research on their efficacy and clinical significance in RA with disruptions to the intestinal microbiota remains limited. In this review, we provide an overview of the concept of postbiotics and summarize the current knowledge regarding postbiotics and their potential use in RA therapy. Postbiotics show potential as a viable adjunctive therapy option for RA.}, }
@article {pmid38029089, year = {2023}, author = {Krishnamurthy, HK and Pereira, M and Bosco, J and George, J and Jayaraman, V and Krishna, K and Wang, T and Bei, K and Rajasekaran, JJ}, title = {Gut commensals and their metabolites in health and disease.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1244293}, pmid = {38029089}, issn = {1664-302X}, abstract = {PURPOSE OF REVIEW: This review comprehensively discusses the role of the gut microbiome and its metabolites in health and disease and sheds light on the importance of a holistic approach in assessing the gut.<br><br>RECENT FINDINGS: The gut microbiome consisting of the bacteriome, mycobiome, archaeome, and virome has a profound effect on human health. Gut dysbiosis which is characterized by perturbations in the microbial population not only results in gastrointestinal (GI) symptoms or conditions but can also give rise to extra-GI manifestations. Gut microorganisms also produce metabolites (short-chain fatty acids, trimethylamine, hydrogen sulfide, methane, and so on) that are important for several interkingdom microbial interactions and functions. They also participate in various host metabolic processes. An alteration in the microbial species can affect their respective metabolite concentrations which can have serious health implications. Effective assessment of the gut microbiome and its metabolites is crucial as it can provide insights into one's overall health.<br><br>SUMMARY: Emerging evidence highlights the role of the gut microbiome and its metabolites in health and disease. As it is implicated in GI as well as extra-GI symptoms, the gut microbiome plays a crucial role in the overall well-being of the host. Effective assessment of the gut microbiome may provide insights into one's health status leading to more holistic care.}, }
@article {pmid37539715, year = {2023}, author = {Berenson, CS and Lashner, B and Korman, LY and Hohmann, E and Deshpande, A and Louie, TJ and Sims, M and Pardi, D and Kraft, CS and Wang, EEL and Cohen, SH and Feuerstadt, P and Oneto, C and Misra, B and Pullman, J and De, A and Memisoglu, A and Lombardi, DA and Hasson, BR and McGovern, BH and von Moltke, L and Lee, CH}, title = {Prevalence of Comorbid Factors in Patients With Recurrent Clostridioides difficile Infection in ECOSPOR III, a Randomized Trial of an Oral Microbiota-Based Therapeutic.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {77}, number = {11}, pages = {1504-1510}, doi = {10.1093/cid/ciad448}, pmid = {37539715}, issn = {1537-6591}, support = {//Seres Therapeutics/ ; }, abstract = {BACKGROUND: Although comorbidities are risk factors for recurrent Clostridioides difficile infection (rCDI), many clinical trials exclude patients with medical conditions such as malignancy or immunosuppression. In a phase 3, double-blind, placebo-controlled, randomized trial (ECOSPOR III), fecal microbiota spores, live (VOWST, Seres Therapeutics; hereafter "VOS," formerly SER-109), an oral microbiota therapeutic, significantly reduced the risk of rCDI at week 8. We evaluated the efficacy of VOS compared with placebo in patients with comorbidities and other risk factors for rCDI.<br><br>METHODS: Adults with rCDI were randomized to receive VOS or placebo (4 capsules daily for 3 days) following standard-of-care antibiotics. In this post hoc analysis, the rate of rCDI through week 8 was assessed in VOS-treated participants compared with placebo for subgroups including (i) Charlson comorbidity index (CCI) score category (0, 1-2, 3-4, &#x2265;5); (ii) baseline creatinine clearance (<30, 30-50, >50 to 80, or >80 mL/minute); (iii) number of CDI episodes, inclusive of the qualifying episode (3 and &#x2265;4); (iv) exposure to non-CDI-targeted antibiotics after dosing; and (v) acid-suppressing medication use at baseline.<br><br>RESULTS: Of 281 participants screened, 182 were randomized (59.9% female; mean age, 65.5 years). Comorbidities were common with a mean overall baseline age-adjusted CCI score of 4.1 (4.1 in the VOS arm and 4.2 in the placebo arm). Across all subgroups analyzed, VOS-treated participants had a lower relative risk of recurrence compared with placebo.<br><br>CONCLUSIONS: In this post hoc analysis, VOS reduced the risk of rCDI compared with placebo, regardless of baseline characteristics, concomitant medications, or comorbidities.}, }
@article {pmid38029086, year = {2023}, author = {Yang, J and He, Y and Liao, X and Hu, J and Li, K}, title = {Does postoperative pulmonary infection correlate with intestinal flora following gastric cancer surgery? - a nested case-control study.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1267750}, doi = {10.3389/fmicb.2023.1267750}, pmid = {38029086}, issn = {1664-302X}, abstract = {INTRODUCTION: The primary objective of this study was to investigate the potential correlation between gut microbes and postoperative pulmonary infection in gastric cancer patients. Additionally, we aimed to deduce the mechanism of differential functional genes in disease progression to gain a better understanding of the underlying pathophysiology.<br><br>METHODS: A nested case-control study design was utilized to enroll patients with gastric cancer scheduled for surgery at West China Hospital of Sichuan University. Patients were categorized into two groups, namely, the pulmonary infection group and the control group, based on the development of postoperative pulmonary infection. Both groups were subjected to identical perioperative management protocols. Fecal samples were collected 24&#x2009;h postoperatively and upon pulmonary infection diagnosis, along with matched controls. The collected samples were subjected to 16S rDNA and metagenomic analyses, and clinical data and blood samples were obtained for further analysis.<br><br>RESULTS: A total of 180 fecal specimens were collected from 30 patients in both the pulmonary infection and control groups for 16S rDNA analysis, and 3 fecal samples from each group were selected for metagenomic analysis. The study revealed significant alterations in the functional genes of the intestinal microbiome in patients with postoperative pulmonary infection in gastric cancer, primarily involving Klebsiella, Enterobacter, Ruminococcus, and Collinsella. During postoperative pulmonary infection, gut flora and inflammatory factors were found to be associated with the lipopolysaccharide synthesis pathway and short-chain fatty acid (SCFA) synthesis pathway.<br><br>DISCUSSION: The study identified enriched populations of Klebsiella, Escherella, and intestinal bacteria during pulmonary infection following gastric cancer surgery. These bacteria were found to regulate the lipopolysaccharide synthesis pathway, contributing to the initiation and progression of pulmonary infections. Inflammation modulation in patients with postoperative pulmonary infection may be mediated by short-chain fatty acids. The study also revealed that SCFA synthesis pathways were disrupted, affecting inflammation-related immunosuppression pathways. By controlling and maintaining intestinal barrier function, SCFAs may potentially reduce the occurrence of pulmonary infections after gastric cancer surgery. These findings suggest that targeting the gut microbiome and SCFA synthesis pathways may be a promising approach for preventing postoperative pulmonary infections in gastric cancer patients.}, }
@article {pmid38029085, year = {2023}, author = {Cronin, P and McCarthy, S and Hurley, C and Ghosh, TS and Cooney, JC and Tobin, AM and Murphy, M and O'Connor, EM and Shanahan, F and O'Toole, PW}, title = {Comparative diet-gut microbiome analysis in Crohn's disease and Hidradenitis suppurativa.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1289374}, doi = {10.3389/fmicb.2023.1289374}, pmid = {38029085}, issn = {1664-302X}, abstract = {INTRODUCTION: The chronic inflammatory skin disease Hidradenitis suppurativa (HS) is strongly associated with Crohn's Disease (CD). HS and CD share clinical similarities and similar inflammatory pathways are upregulated in both conditions. Increased prevalence of inflammatory disease in industrialised nations has been linked to the Western diet. However, gut microbiota composition and diet interaction have not been compared in HS and CD.<br><br>METHODS: Here we compared the fecal microbiota (16S rRNA gene amplicon sequencing) and habitual diet of previously reported subjects with HS (n&#x2009;=&#x2009;55), patients with CD (n&#x2009;=&#x2009;102) and controls (n&#x2009;=&#x2009;95).<br><br>RESULTS AND DISCUSSION: Patients with HS consumed a Western diet similar to patients with CD. Meanwhile, habitual diet in HS and CD was significantly different to controls. Previously, we detected differences in microbiota composition among patients with HS from that of controls. We now show that 40% of patients with HS had a microbiota configuration similar to that of CD, characterised by the enrichment of pathogenic genera (Enterococcus, Veillonella and Escherichia_Shigella) and the depletion of putatively beneficial genera (Faecalibacterium). The remaining 60% of patients with HS harboured a normal microbiota similar to that of controls. Antibiotics, which are commonly used to treat HS, were identified as a co-varying with differences in microbiota composition. We examined the levels of several inflammatory markers highlighting that growth-arrest specific 6 (Gas6), which has anti-inflammatory potential, were significantly lower in the 40% of patients with HS who had a CD microbiota configuration. Levels of the pro-inflammatory cytokine IL-12, which is a modulator of intestinal inflammation in CD, were negatively correlated with the abundance of health-associated genera in patients with HS. In conclusion, the fecal microbiota may help identify patients with HS who are at greater risk for development of CD.}, }
@article {pmid38029083, year = {2023}, author = {Khairunisa, BH and Heryakusuma, C and Ike, K and Mukhopadhyay, B and Susanti, D}, title = {Evolving understanding of rumen methanogen ecophysiology.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1296008}, doi = {10.3389/fmicb.2023.1296008}, pmid = {38029083}, issn = {1664-302X}, abstract = {Production of methane by methanogenic archaea, or methanogens, in the rumen of ruminants is a thermodynamic necessity for microbial conversion of feed to volatile fatty acids, which are essential nutrients for the animals. On the other hand, methane is a greenhouse gas and its production causes energy loss for the animal. Accordingly, there are ongoing efforts toward developing effective strategies for mitigating methane emissions from ruminant livestock that require a detailed understanding of the diversity and ecophysiology of rumen methanogens. Rumen methanogens evolved from free-living autotrophic ancestors through genome streamlining involving gene loss and acquisition. The process yielded an oligotrophic lifestyle, and metabolically efficient and ecologically adapted descendants. This specialization poses serious challenges to the efforts of obtaining axenic cultures of rumen methanogens, and consequently, the information on their physiological properties remains in most part inferred from those of their non-rumen representatives. This review presents the current knowledge of rumen methanogens and their metabolic contributions to enteric methane production. It also identifies the respective critical gaps that need to be filled for aiding the efforts to mitigate methane emission from livestock operations and at the same time increasing the productivity in this critical agriculture sector.}, }
@article {pmid38029079, year = {2023}, author = {Koepper, S and Clark, KF and McClure, JT and Revie, CW and Stryhn, H and Thakur, KK}, title = {Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1245818}, doi = {10.3389/fmicb.2023.1245818}, pmid = {38029079}, issn = {1664-302X}, abstract = {The shell microbial community of lobsters-a key factor in the development of epizootic shell disease (ESD)-is still insufficiently researched in Atlantic Canada and many knowledge gaps remain. This study aimed to establish a baseline description and analysis of the shell microbiome of apparently healthy lobsters from four locations in the region. More than 180 lobster shell swab samples were collected from New Brunswick, Nova Scotia and Prince Edward Island (PEI). PacBio long-read 16S rDNA sequencing and bioinformatic analyses in QIIME2 identified the shell-associated bacteria. The shell microbiome of healthy lobsters consisted mainly of the bacterial classes Gammaproteobacteria, Saprospiria, Verrucomicrobiae, Alphaproteobacteria, Flavobacteriia, Acidimicrobiia and Planctomycetia. The microbial composition differed regionally and seasonally, with some classes showing decreased or increased relative abundances in the PEI samples as well as in the winter and spring samples in Nova Scotia. The core shell microbiome included potentially pathogenic as well as beneficial bacterial taxa, of which some were present only in certain regions. Bacterial taxa that have previously been associated with ESD were present on healthy lobsters in Atlantic Canada, but their frequency differed by location, sampling time, and moult stage. This study indicated that geographical and seasonal factors influenced the shell microbiome of apparently healthy lobsters more than host factors such as sex, size, and moult stage. Our results provide valuable reference microbial data from lobsters in a disease-free state.}, }
@article {pmid38029074, year = {2023}, author = {Frąszczak, K and Barczyński, B and Siwiec, R and Kondracka, A and Malm, A and Kotarski, J and Witt, E and Korona-Głowniak, I}, title = {The analysis of Lactobacillus spp. distribution in the vaginal microbiota of Polish women with abnormal Pap smear result.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1257587}, doi = {10.3389/fmicb.2023.1257587}, pmid = {38029074}, issn = {1664-302X}, abstract = {INTRODUCTION: A healthy vaginal microbiota is represented mainly by Lactobacillus spp. and plays a vital role in maintaining the functional balance in the vaginal environment. Scientists have drawn attention to possible correlations between the vaginal microbiome and gynecological neoplasms. Several recent studies have shown a potential link between the vaginal microbiome and the risk of developing cervical cancer from human papillomavirus (HPV) infection. This study aimed to compare the prevalence and abundance of various lactic acid bacteria species (LABs) in vaginal swabs from healthy controls and patients with abnormal Pap smear results.<br><br>METHODS: The study included 100 women (79 patients with abnormal cervical Pap smear results and 21 controls) from whom vaginal swabs were collected. Real-time quantitative PCR was used to determine seven lactic acid bacteria (LAB) species and their quantities.<br><br>RESULTS: Most patients were colonized by two Lactobacillus species, primarily Lactobacillus gasseri (93%) and L. crispatus (83%). Patient age and place of residence were associated with the diversity of LAB in the vaginal microbiota. The abundance of L. delbrueckii in the vaginal microbiota increased, whereas the abundance of L. gasseri abundance decreased, with patient age. Lactobacillus acidophilus and Limosilactobacillus fermentum were significantly more often detected in patients living in rural versus urban areas. Statistical analysis did not show any significant differences in LAB between groups of patients with various changes on smear tests.<br><br>DISCUSSION: The degree of dysplastic changes in the endothelium or the presence of a group of atypical cervical stratified epithelial cells was not associated with significant changes in the studied vaginal bacteria.}, }
@article {pmid38029073, year = {2023}, author = {Xie, Q and Hu, B}, title = {Effects of gut microbiota on prostatic cancer: a two-sample Mendelian randomization study.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1250369}, doi = {10.3389/fmicb.2023.1250369}, pmid = {38029073}, issn = {1664-302X}, abstract = {AIM: Recent observational and small-sample case-control studies have shown a relationship between gut microbiota composition and prostatic cancer (PCa). Nevertheless, the causal association between gut microbiota and PCa is still unclear. Herein, we used the Mendelian randomization (MR) method to explore the potential causal relationship between gut microbiota and PCa.<br><br>METHODS: In this two-sample MR study, data were extracted from the summary statistics of gut microbiota from the largest available genome-wide association study meta-analysis conducted by the MiBioGen consortium (n = 14,306) and the Dutch Microbiome Project (n = 8,208). Summary statistics for PCa were obtained from the FinnGen consortium release data (n = 95,213). Inverse variance weighted (IVW), MR-Egger, strength test (F), and MR-PRESSO were used to examine the potential causal association between gut microbiota and PCa. Cochran's Q statistics were used to quantify the heterogeneity of instrumental variables.<br><br>RESULTS: IVW estimates suggested that the relative abundance of Akkermansia muciniphila (odds ratio [OR] = 0.7926, 95% confidence interval [CI]: 0.6655-0.9440) and Bacteroides salyersiae (OR = 0.9023, 95% CI: 0.8262-0.9853) were negatively associated with the odds of PCa, while that of Eubacterium biforme (OR = 1.1629, 95% CI: 1.0110-1.3376) was positively associated with the odds of PCa. In addition, we explored these relationships among patients without other cancers and similarly found that the relative abundance of Akkermansia muciniphila, Bacteroides salyersiae, and Eubacterium biforme were linked to PCa (all P < 0.05).<br><br>CONCLUSION: Gut microbiota potentially influenced the occurrence of PCa. Our findings may provide some new ideas for researching the methods of PCa prevention. In addition, further studies are needed to explore the causal association and specific underlying mechanisms between gut microbiota and PCa.}, }
@article {pmid38029072, year = {2023}, author = {Dreyer, A and Lenz, C and Groß, U and Bohne, W and Zautner, AE}, title = {Characterization of Campylobacter jejuni proteome profiles in co-incubation scenarios.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1247211}, doi = {10.3389/fmicb.2023.1247211}, pmid = {38029072}, issn = {1664-302X}, abstract = {In dynamic microbial ecosystems, bacterial communication is a relevant mechanism for interactions between different microbial species. When C. jejuni resides in the intestine of either avian or human hosts, it is exposed to diverse bacteria from the microbiome. This study aimed to reveal the influence of co-incubation with Enterococcus faecalis, Enterococcus faecium, or Staphylococcus aureus on the proteome of C. jejuni 81-176 using data-independent-acquisition mass spectrometry (DIA-MS). We compared the proteome profiles during co-incubation with the proteome profile in response to the bile acid deoxycholate (DCA) and investigated the impact of DCA on proteomic changes during co-incubation, as C. jejuni is exposed to both factors during colonization. We identified 1,375 proteins by DIA-MS, which is notably high, approaching the theoretical maximum of 1,645 proteins. S. aureus had the highest impact on the proteome of C. jejuni with 215 up-regulated and 230 down-regulated proteins. However, these numbers are still markedly lower than the 526 up-regulated and 516 down-regulated proteins during DCA exposure. We identified a subset of 54 significantly differentially expressed proteins that are shared after co-incubation with all three microbial species. These proteins were indicative of a common co-incubation response of C. jejuni. This common proteomic response partly overlapped with the DCA response; however, several proteins were specific to the co-incubation response. In the co-incubation experiment, we identified three membrane-interactive proteins among the top 20 up-regulated proteins. This finding suggests that the presence of other bacteria may contribute to increased adherence, e.g., to other bacteria but eventually also epithelial cells or abiotic surfaces. Furthermore, a conjugative transfer regulon protein was typically up-expressed during co-incubation. Exposure to both, co-incubation and DCA, demonstrated that the two stressors influenced each other, resulting in a unique synergistic proteomic response that differed from the response to each stimulus alone. Data are available via ProteomeXchange with identifier PXD046477.}, }
@article {pmid38028745, year = {2023}, author = {Kural-Rendon, C and Ford, NE and Wagner, MR}, title = {Interactions with fungi vary among Tripsacum dactyloides genotypes from across a precipitation gradient.}, journal = {AoB PLANTS}, volume = {15}, number = {6}, pages = {plad072}, doi = {10.1093/aobpla/plad072}, pmid = {38028745}, issn = {2041-2851}, abstract = {Plant-associated microbes, specifically fungal endophytes, augment the ability of many grasses to adapt to extreme environmental conditions. Tripsacum dactyloides (Eastern gamagrass) is a perennial, drought-tolerant grass native to the tallgrass prairies of the central USA. The extent to which the microbiome of T. dactyloides contributes to its drought tolerance is unknown. Ninety-seven genotypes of T. dactyloides were collected from native populations across an east-west precipitation gradient in Kansas, Oklahoma and Texas, and then grown together in a common garden for over 20 years. Root and leaf samples were visually examined for fungal density. Because fungal endophytes confer drought-tolerant capabilities to their host plants, we expected to find higher densities of fungal endophytes in plants from western, drier regions, compared to plants from eastern, wetter regions. Results confirmed a negative correlation between endophyte densities in roots and precipitation at the genotype's original location (r = -0.21 P = 0.04). Our analyses reveal that the host genotype's origin along the precipitation gradient predicts the absolute abundance of symbionts in the root, but not the relative abundances of particular organisms or the overall community composition. Overall, these results demonstrate that genetic variation for plant-microbe interactions can reflect historical environment, and reinforce the importance of considering plant genotype in conservation and restoration work in tallgrass prairie ecosystems.}, }
@article {pmid38028558, year = {2023}, author = {O'Shaughnessy, R and Common, J and Gutowska-Owsiak, D}, title = {Editorial: Novel aspects of the immunological and structural barrier of the epidermis.}, journal = {Frontiers in molecular biosciences}, volume = {10}, number = {}, pages = {1324920}, doi = {10.3389/fmolb.2023.1324920}, pmid = {38028558}, issn = {2296-889X}, }
@article {pmid38028206, year = {2023}, author = {Chai, J and Long, X and Wu, P and Wang, J and Wu, X and Tu, Z and Wei, M and Guo, Z and Zhang, T and Chen, L}, title = {Lactobacillus sp. participated in the adaptation of Rongchang piglets to cold stress.}, journal = {Veterinarni medicina}, volume = {68}, number = {10}, pages = {392-402}, doi = {10.17221/54/2023-VETMED}, pmid = {38028206}, issn = {0375-8427}, abstract = {Rongchang piglets were easily induced to cold stress and diarrhoea in the winter when raised in an open hog house. However, they also gradually recovered under mid-cold stress. Other studies have suggested gut microbiome might be involved in the host energy metabolism to relieve stress. To study how to adapt Rongchang piglets to cold stress by gut microbiome, thirty Rongchang piglets were randomly divided into a mild cold stress group and a control group for 30 consecutive days. The findings revealed that the piglets had low growth performance and a high diarrhoea rate and mortality rate during the first half of the cold treatment, but subsequently stabilised. The level of cortisol (COR) also displayed a similar trend. In the mild cold stress group, the relative abundance of Muribaculaceae significantly increased on day 15, and the predominant bacterial on day 30 was Lactobacillus sp. Our results indicated that the Rongchang piglet's production performance and health were impaired at the start of the mild cold stress. However, as time passed, the body could progressively adapt to the low temperature, and Lactobacillus sp. participated in this process. This study provides new insight into how to alleviate health damage caused by cold stress.}, }
@article {pmid38028014, year = {2023}, author = {Liu, W and Peng, L and Chen, L and Wan, J and Lou, S and Yang, T and Shen, Z}, title = {Skin microbial dysbiosis is a characteristic of systemic drug-related intertriginous and flexural exanthema-like lesions induced by EGFR inhibitor.}, journal = {Heliyon}, volume = {9}, number = {11}, pages = {e21690}, doi = {10.1016/j.heliyon.2023.e21690}, pmid = {38028014}, issn = {2405-8440}, abstract = {OBJECTIVES: To investigate the characteristics of the skin microbiome in severe afatinib-induced skin toxicity.<br><br>METHODS: Body site-matched skin surface samples were collected from the lesions on seven flexural sites of one lung cancer (Patient 1) with serious systemic drug-related intertriginous and flexural exanthema (SDRIFE)-like toxicity induced by EGFR-TKI and three healthy age/sex matched controls for whole metagenomics sequencing analysis. Lung cancer Patient 1 and Patient 2 were prescribed minocycline and followed up.<br><br>RESULTS: In SDRIFE-like toxicities induced by afatinib, lesion microbiota richness (ACE and Chao1 index: p&#xa0;<&#xa0;0.001) and diversity (Shannon's and Simpson's diversity indices: p&#xa0;<&#xa0;0.01) were reduced. Similarly, the beta diversity analysis (R&#xa0;=&#xa0;1, p&#xa0;=&#xa0;0.002 for ANOSIM) showed that the apparent difference in the microbiota composition was statistically significant. The microbial taxa composition in the patient showed an increased abundance of pathogenic bacteria and a decreased abundance of commensal bacteria. LEfSe analysis identified strong bacterial pathogenicity in the patient, while healthy controls exhibited enrichment in several pathways that are beneficial for skin commensal bacteria and skin physiology, including key amino acid metabolism, energy/lipid/glycan biosynthesis/metabolism, and cofactors/vitamins biosynthesis. Ultimately, the patients experienced significant improvement with minocycline.<br><br>CONCLUSION: Microbial dysbiosis is a characteristic of severe SDRIFE-like toxicity induced by afatinib.}, }
@article {pmid38027512, year = {2023}, author = {Barton, JR and Londregan, AK and Alexander, TD and Entezari, AA and Covarrubias, M and Waldman, SA}, title = {Enteroendocrine cell regulation of the gut-brain axis.}, journal = {Frontiers in neuroscience}, volume = {17}, number = {}, pages = {1272955}, doi = {10.3389/fnins.2023.1272955}, pmid = {38027512}, issn = {1662-4548}, abstract = {Enteroendocrine cells (EECs) are an essential interface between the gut and brain that communicate signals about nutrients, pain, and even information from our microbiome. EECs are hormone-producing cells expressed throughout the gastrointestinal epithelium and have been leveraged by pharmaceuticals like semaglutide (Ozempic, Wegovy), terzepatide (Mounjaro), and retatrutide (Phase 2) for diabetes and weight control, and linaclotide (Linzess) to treat irritable bowel syndrome (IBS) and visceral pain. This review focuses on role of intestinal EECs to communicate signals from the gut lumen to the brain. Canonically, EECs communicate information about the intestinal environment through a variety of hormones, dividing EECs into separate classes based on the hormone each cell type secretes. Recent studies have revealed more diverse hormone profiles and communication modalities for EECs including direct synaptic communication with peripheral neurons. EECs known as neuropod cells rapidly relay signals from gut to brain via a direct communication with vagal and primary sensory neurons. Further, this review discusses the complex information processing machinery within EECs, including receptors that transduce intraluminal signals and the ion channel complement that govern initiation and propagation of these signals. Deeper understanding of EEC physiology is necessary to safely treat devastating and pervasive conditions like irritable bowel syndrome and obesity.}, }
@article {pmid38027267, year = {2023}, author = {Francis, D and Chawla, A and LaComb, JF and Markarian, K and Robertson, CE and Frank, DN and Gathungu, GN}, title = {Gastroesophageal reflux and PPI exposure alter gut microbiota in very young infants.}, journal = {Frontiers in pediatrics}, volume = {11}, number = {}, pages = {1254329}, doi = {10.3389/fped.2023.1254329}, pmid = {38027267}, issn = {2296-2360}, abstract = {IMPORTANCE: Infants with symptomatic Gastroesophageal reflux are treated with pharmacological therapy that includes proton pump inhibitors (PPI) with clinical improvement. The alterations to gut microbiome profiles in comparison to infants without reflux is not known.<br><br>OBJECTIVE: To determine the effect of PPI therapy on gut bacterial richness, diversity, and proportions of specific taxa in infants when compared to infants not exposed to acid suppressive therapy.<br><br>This cohort study was conducted at the Stony Brook Hospital in Stony Brook, NY between February 2016, and June 2019. Infants meeting inclusion criteria were enrolled in a consecutive fashion.<br><br>RESULTS: A total of 76 Infants were recruited and 60 were enrolled in the study, Twenty nine infants met clinical criteria for reflux and were treated with PPI therapy: median [IQR] gestation: 38.0 weeks [34.7-39.6 weeks]; median [IQR] birthweight: 2.95&#x2005;Kg [2.2-3.4]; 14 [46.7%] male) and 29 infant were healthy controls median [IQR] gestation: 39.1 weeks [38-40 weeks]; median [IQR] birthweight: 3.3&#x2005;Kg [2.2-3.4]; 17 [58.6%] male); 58 stool samples from 58 infants were analyzed. There were differences in Shannon diversity between the reflux and control groups. The reflux group that was exposed to PPI therapy had increased relative abundance of a diverse set of genera belonging to the phylum Firmicutes. On the other hand, the control group microbiota was dominated by Bifidobacterium, and a comparatively lower level of enrichment and abundance of microbial taxa was observed in this group of infants.<br><br>CONCLUSIONS AND RELEVANCE: We observed significant differences in both &#x3b1;- and &#x3b2;-diversity of the microbiome, when the two groups of infants were compared. The microbiome in the reflux group had more bacterial taxa and the duration of PPIs exposure was clearly associated with the diversity and abundance of gut microbes. These findings suggest that PPI exposure among infants results in early enrichment of the intestinal microbiome.}, }
@article {pmid38027226, year = {2023}, author = {Tang, J and Han, Y and Pei, L and Gu, W and Qiu, R and Wang, S and Ma, Q and Gan, Y and Tang, M}, title = {Comparative analysis of the rhizosphere microbiome and medicinally active ingredients of Atractylodes lancea from different geographical origins.}, journal = {Open life sciences}, volume = {18}, number = {1}, pages = {20220769}, doi = {10.1515/biol-2022-0769}, pmid = {38027226}, issn = {2391-5412}, abstract = {This study aimed to explore the important role of the rhizosphere microbiome in the quality of Atractylodes lancea (Thunb.) DC. (A. lancea). The rhizosphere microbial community of A. lancea at two sampling sites was studied using metagenomic technology. The results of α-diversity analysis showed that the rhizosphere microbial richness and diversity were higher in the Maoshan area. The higher abundance of core microorganisms of the rhizosphere, especially Penicillium and Streptomyces, in the Maoshan area compared with those in the Yingshan area might be an important factor affecting the yield of A. lancea. Redundancy analysis illustrated that the available phosphorus had a significant effect on the rhizosphere microbial community structure of A. lancea. We also showed that the plant-microbe and microbe-microbe interactions were closer in the Maoshan area than in the Yingshan area, and Streptomyces were the main contributors to the potential functional difference between the two regions. A. lancea in the Maoshan area had a high content of atractylodin and atractylon, which might be related to the enhanced abundance of Streptomyces, Candidatus-Solibacter, and Frankia. Taken together, this study provided theoretical insights into the interaction between medicinal plants and the rhizosphere microbiome and provides a valuable reference for studying beneficial microbes of A. lancea.}, }
@article {pmid38027221, year = {2023}, author = {Nie, D and Li, C and Zhang, Y}, title = {PitNETs and the gut microbiota: potential connections, future directions.}, journal = {Frontiers in endocrinology}, volume = {14}, number = {}, pages = {1255911}, doi = {10.3389/fendo.2023.1255911}, pmid = {38027221}, issn = {1664-2392}, abstract = {The role of the gut microbiome has been widely discussed in numerous works of literature. The biggest concern is the association of the gut microbiome with the central nervous system through the microbiome-brain-gut axis in the past ten years. As more and more research has been done on the relationship between the disease of the central nervous system and gut microbes. This fact is being revealed that gut microbes seem to play an important role from the onset and progression of the disease to clinical symptoms, and new treatments. As a special tumor of the central nervous system, pituitary neuroendocrine tumors (PitNETs)are closely related to metabolism, endocrinology, and immunity. These factors are the vectors through which intestinal microbes interact with the central nervous system. However, little is known about the effects of gut microbes on the PitNET. In this review, the relationship of gut microbiota in PitNETs is introduced, the potential effects of the gut-brain axis in this relationship are analyzed, and future research directions are presented.}, }
@article {pmid38027173, year = {2023}, author = {Aghajanova, L and Altmäe, S and Sokalska, A}, title = {Editorial: Uterine factors associated with fertility impairment.}, journal = {Frontiers in endocrinology}, volume = {14}, number = {}, pages = {1307237}, doi = {10.3389/fendo.2023.1307237}, pmid = {38027173}, issn = {1664-2392}, }
@article {pmid38027009, year = {2023}, author = {Feng, Y and Xu, D}, title = {Short-chain fatty acids are potential goalkeepers of atherosclerosis.}, journal = {Frontiers in pharmacology}, volume = {14}, number = {}, pages = {1271001}, doi = {10.3389/fphar.2023.1271001}, pmid = {38027009}, issn = {1663-9812}, abstract = {Short-chain fatty acids (SCFAs) are metabolites produced by gut bacteria and play a crucial role in various inflammatory diseases. Increasing evidence suggests that SCFAs can improve the occurrence and progression of atherosclerosis. However, the molecular mechanisms through which SCFAs regulate the development of atherosclerosis have not been fully elucidated. This review provides an overview of the research progress on SCFAs regarding their impact on the risk factors and pathogenesis associated with atherosclerosis, with a specific focus on their interactions with the endothelium and immune cells. These interactions encompass the inflammation and oxidative stress of endothelial cells, the migration of monocytes/macrophages, the lipid metabolism of macrophages, the proliferation and migration of smooth muscle cells, and the proliferation and differentiation of Treg cells. Nevertheless, the current body of research is insufficient to comprehensively understand the full spectrum of SCFAs' mechanisms of action. Therefore, further in-depth investigations are imperative to establish a solid theoretical foundation for the development of clinical therapeutics in this context.}, }
@article {pmid38026977, year = {2023}, author = {Zhou, J and Liu, J and Lin, Q and Shi, L and Zeng, Z and Guan, L and Ma, Y and Zeng, Y and Zhong, S and Xu, L}, title = {Characteristics of the gut microbiome and metabolic profile in elderly patients with sarcopenia.}, journal = {Frontiers in pharmacology}, volume = {14}, number = {}, pages = {1279448}, doi = {10.3389/fphar.2023.1279448}, pmid = {38026977}, issn = {1663-9812}, abstract = {Introduction: There is growing evidence of research indicating that the gut microbiota is involved in the development of sarcopenia. Nevertheless, there exists a notable deficiency in comprehension concerning the connection between irregularities in the intestinal microbiome and metabolic processes in older individuals suffering from sarcopenia. Methods: To analyze fecal samples obtained from a cohort of 30 older patients diagnosed with sarcopenia as well as 30 older patients without sarcopenia, this study employed 16S rDNA sequencing and liquid chromatography-mass spectrometry (LC-MS)-based non-targeted metabolomics profiling techniques. Results: As a result, we found that 29 genera and 172 metabolites were significantly altered in the sarcopenic patients. Among them, Blautia, Lachnospiraceae_unclassified, and Subdoligranulum were the bacteria with a potential diagnostic value for sarcopenia diagnosis. Correlation analysis between clinical indices and these gut bacteria suggested that the IL-6 level was negatively correlated with Blautia. Function prediction analysis demonstrated that 17 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways differ significantly between sarcopenic and non-sarcopenic patients. The primary classes of metabolites identified in the study included lipids and lipid-like molecules, organic acids and derivatives, and organoheterocyclic compounds. KEGG enrichment analysis showed that purine metabolism, arginine and proline metabolism, alanine, aspartate, and glutamate metabolism, butanoate metabolism, and histidine metabolism may contribute to the development of sarcopenia. The correlation study on gut microbiota and metabolites found that Lachnospiraceae_unclassified was positively associated with seven metabolites that were more abundant in the non-sarcopenia group and negatively correlated with three metabolites that were more abundant in the sarcopenia group. In addition, Subdoligranulum was positively correlated with seven metabolites that were lacking in sarcopenia and negatively correlated with two metabolites that were enriching in sarcopenia. Moreover, Blautia was positively associated with xanthosine. Discussion: We conducted a study on the intestinal microbiota and metabolic profile of elderly individuals with sarcopenia, offering a comprehensive analysis of the overall ecosystem. Through this investigation, we were able to validate existing research on the gut-muscle axis and further investigate potential pathogenic processes and treatment options for sarcopenia.}, }
@article {pmid38026796, year = {2023}, author = {Pohlin, F and Frei, C and Meyer, LCR and Roch, FF and Quijada, NM and Conrady, B and Neubauer, V and Hofmeyr, M and Cooper, D and Stalder, G and Wetzels, SU}, title = {Capture and transport of white rhinoceroses (Ceratotherium simum) cause shifts in their fecal microbiota composition towards dysbiosis.}, journal = {Conservation physiology}, volume = {11}, number = {1}, pages = {coad089}, doi = {10.1093/conphys/coad089}, pmid = {38026796}, issn = {2051-1434}, abstract = {Translocations of Rhinocerotidae are commonly performed for conservation purposes but expose the animals to a variety of stressors (e.g. prolonged fasting, confinement, novel environment, etc.). Stress may change the composition of gut microbiota, which can impact animal health and welfare. White rhinoceroses in particular can develop anorexia, diarrhea and enterocolitis after translocation. The aim of this study was to investigate the associations of age, sex and translocation on the rhinoceros' fecal bacterial microbiota composition. fecal samples were collected from rhinoceroses at capture (n = 16) and after a >30-hour road transport (n = 7). DNA was isolated from these samples and submitted for 16S rRNA V3-V4 phylotyping. Alpha diversity indices of the rhinoceros' fecal microbiota composition of different age, sex and before and after transport were compared using non-parametric statistical tests and beta diversity indices using Permutational Multivariate Analysis Of Variance (PERMANOVA). Resulting P-values were alpha-corrected (Padj.). Alpha and beta diversity did not differ between rhinoceroses of different age and sex. However, there was a significant difference in beta diversity between fecal samples collected from adult animals at capture and after transport. The most abundant bacterial phyla in samples collected at capture were Firmicutes and Bacteroidetes (85.76%), represented by Lachnospiraceae, Ruminococcaceae and Prevotellaceae families. The phyla Proteobacteria (Padj. = 0.009) and Actinobacteria (Padj. = 0.012), amongst others, increased in relative abundance from capture to after transport encompassing potentially pathogenic bacterial families such as Enterobacteriaceae (Padj. = 0.018) and Pseudomonadaceae (Padj. = 0.022). Important commensals such as Spirochaetes (Padj. = 0.009), Fibrobacteres (Padj. = 0.018) and Lachnospiraceae (Padj. = 0.021) decreased in relative abundance. These results indicate that the stressors associated with capture and transport cause an imbalanced fecal microbiota composition in white rhinoceroses that may lead to potentially infectious intestinal disorders. This imbalance may result from recrudescence of normally innocuous pathogens, increased shedding of pathogens or increased vulnerability to new pathogens.}, }
@article {pmid38026235, year = {2023}, author = {McCall, KD and Walter, D and Patton, A and Thuma, JR and Courreges, MC and Palczewski, G and Goetz, DJ and Bergmeier, S and Schwartz, FL}, title = {Anti-Inflammatory and Therapeutic Effects of a Novel Small-Molecule Inhibitor of Inflammation in a Male C57BL/6J Mouse Model of Obesity-Induced NAFLD/MAFLD.}, journal = {Journal of inflammation research}, volume = {16}, number = {}, pages = {5339-5366}, doi = {10.2147/JIR.S413565}, pmid = {38026235}, issn = {1178-7031}, abstract = {PURPOSE: Non-alcoholic fatty liver disease (NAFLD), recently renamed metabolic (dysfunction) associated fatty liver disease (MAFLD), is the most common chronic liver disease in the United States. Presently, there is an intense and ongoing effort to identify and develop novel therapeutics for this disease. In this study, we explored the anti-inflammatory activity of a new compound, termed IOI-214, and its therapeutic potential to ameliorate NAFLD/MAFLD in male C57BL/6J mice fed a high fat (HF) diet.<br><br>METHODS: Murine macrophages and hepatocytes in culture were treated with lipopolysaccharide (LPS) &#xb1; IOI-214 or DMSO (vehicle), and RT-qPCR analyses of inflammatory cytokine gene expression were used to assess IOI-214's anti-inflammatory properties in vitro. Male C57BL/6J mice were also placed on a HF diet and treated once daily with IOI-214 or DMSO for 16 weeks. Tissues were collected and analyzed to determine the effects of IOI-214 on HF diet-induced NAFL D/MAFLD. Measurements such as weight, blood glucose, serum cholesterol, liver/serum triglyceride, insulin, and glucose tolerance tests, ELISAs, metabolomics, Western blots, histology, gut microbiome, and serum LPS binding protein analyses were conducted.<br><br>RESULTS: IOI-214 inhibited LPS-induced inflammation in macrophages and hepatocytes in culture and abrogated HF diet-induced mesenteric fat accumulation, hepatic inflammation and steatosis/hepatocellular ballooning, as well as fasting hyperglycemia without affecting insulin resistance or fasting insulin, cholesterol or TG levels despite overall obesity in vivo in male C57BL/6J mice. IOI-214 also decreased systemic inflammation in vivo and improved gut microbiota dysbiosis and leaky gut.<br><br>CONCLUSION: Combined, these data indicate that IOI-214 works at multiple levels in parallel to inhibit the inflammation that drives HF diet-induced NAFLD/MAFLD, suggesting that it may have therapeutic potential for NAFLD/MAFLD.}, }
@article {pmid38026003, year = {2023}, author = {Beretta, S and Apparicio, M and Toniollo, GH and Cardozo, MV}, title = {The importance of the intestinal microbiota in humans and dogs in the neonatal period.}, journal = {Animal reproduction}, volume = {20}, number = {3}, pages = {e20230082}, doi = {10.1590/1984-3143-AR2023-0082}, pmid = {38026003}, issn = {1984-3143}, abstract = {The neonatal period represents a critical stage for the establishment and development of the gut microbiota, which profoundly influences the future health trajectory of individuals. This review examines the importance of intestinal microbiota in humans and dogs, aiming to elucidate the distinct characteristics and variations in the composition between these two species. In humans, the intestinal microbiota contributes to several crucial physiological processes, including digestion, nutrient absorption, immune system development, and modulation of host metabolism. Dysbiosis, an imbalance or disruption of the gut microbial community, has been linked to various disorders, such as inflammatory bowel disease, obesity, and even neurological conditions. Furthermore, recent research has unveiled the profound influence of the gut-brain axis, emphasizing the bidirectional communication between the gut microbiota and the central nervous system, impacting cognitive function and mental health. Similarly, alterations in the canine intestinal microbiota have been associated with gastrointestinal disorders, including chronic enteropathy, such as inflammatory bowel disease, food allergies, and ulcerative histiocytic colitis. However, our understanding of the intricacies and functional significance of the intestinal microbiota in dogs remains limited. Understanding the complex dynamics of the intestinal microbiota in both humans and dogs is crucial for devising effective strategies to promote health and manage disease. Moreover, exploring the similarities and differences in the gut microbial composition between these two species can facilitate translational research, potentially leading to innovative therapeutic interventions and strategies to enhance the well-being of both humans and dogs.}, }
@article {pmid38025771, year = {2023}, author = {Shadid, ILC and Lee-Sarwar, K and Lu, Z and Yadama, A and Laranjo, N and Carey, V and O'Connor, GT and Zeiger, RS and Bacharier, L and Guchelaar, HJ and Liu, YY and Litonjua, AA and Weiss, ST and Mirzakhani, H}, title = {Early life gut microbiome in children following spontaneous preterm birth and maternal preeclampsia.}, journal = {iScience}, volume = {26}, number = {12}, pages = {108311}, doi = {10.1016/j.isci.2023.108311}, pmid = {38025771}, issn = {2589-0042}, abstract = {The early life microbiome plays an important role in developmental and long-term health outcomes. However, it is unknown whether adverse pregnancy complications affect the offspring's gut microbiome postnatally and in early years. In a longitudinal cohort with a five-year follow-up of mother-child pairs affected by preeclampsia (PE) or spontaneous preterm birth (sPTB), we evaluated offspring gut alpha and beta diversity as well as taxa abundances considering factors like breastfeeding and mode of delivery. Our study highlights a trend where microbiome diversity exhibits comparable development across adverse and normal pregnancies. However, specific taxa at genus level emerge with distinctive abundances, showing enrichment and/or depletion over time in relation to PE or sPTB. These findings underscore the potential for certain adverse pregnancy complications to induce alterations in the offspring's microbiome over the course of early life. The implications of these findings on the immediate and long-term health of offspring should be investigated in future studies.}, }
@article {pmid38025767, year = {2023}, author = {Sun, H and Su, X and Liu, Y and Li, G and Du, Q}, title = {Roseburia intestinalis relieves intrahepatic cholestasis of pregnancy through bile acid/FXR-FGF15 in rats.}, journal = {iScience}, volume = {26}, number = {12}, pages = {108392}, doi = {10.1016/j.isci.2023.108392}, pmid = {38025767}, issn = {2589-0042}, abstract = {Previous research has demonstrated significant differences in intestinal flora between pregnant women with intrahepatic cholestasis of pregnancy (ICP) and healthy pregnant women. The objective of our study is to identify the key bacteria involved in ICP rats and explore the underlying mechanism. We established an ICP rat model and collected rat feces for metagenomic sequencing and found that Roseburia intestinalis (R.I) is the key bacteria in ICP. Transplantation of R.I improved phenotypes associated with ICP through the bile acid/farnesoid X receptor-fibroblast growth factor 15 (FXR-FGF15) signaling pathway. We used the FXR antagonist Z-Guggulsterone (Z-Gu) to verify the key role of FXR in ICP and found that Z-Gu reversed the benefits of R.I on ICP rats. Our research highlights the important role of intestinal flora in the pathogenesis of ICP and provides a novel approach for its treatment.}, }
@article {pmid38025669, year = {2023}, author = {Kim, HY and Kim, TH and Shin, JH and Cho, K and Ha, HK and Lee, A and Kim, YJ}, title = {Navigating the microbial community in the trachea-oropharynx of breast cancer patients with or without neoadjuvant chemotherapy (NAC) via endotracheal tube: has NAC caused any change?.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16366}, doi = {10.7717/peerj.16366}, pmid = {38025669}, issn = {2167-8359}, abstract = {BACKGROUND: We compare the diversity and niche specificity of the microbiome in the trachea-oropharynx microbiome of malignant breast neoplasm with or without neoadjuvant chemotherapy (NAC) via NGS analysis.<br><br>METHODS: We prospectively collected a total of 40 endotracheal tubes intubated from subjects, of whom 20 with NAC treated breast cancer (NAC group) and 20 with breast cancer without NAC (Non-NAC group). We generated 16S rRNA-based microbial profiles in IlluminaTM platform and alpha diversity indices were compared between groups. For the comparison of taxa abundance, linear discriminant analysis effect size method with Kruskal-Wallis test was used. The distribution of variables between the two groups was compared using the Mann-Whitney test. For beta diversity analysis, PERMANOVA was used.<br><br>RESULTS: Among the diversity indices, the NAC group showed significantly lower Chao1, Inverse Simpson, and Shannon indices than the Non-NAC group. The three most frequent taxa of all two groups were Streptococcus (20.4%), followed by Veillonella (11.9%), and Prevorella (10.4%). This order was the same in NAC and non-NAC groups.<br><br>CONCLUSION: Here, we provide the first comparison data of the respiratory tract microbiome of breast cancer patients with or without NAC via NGS analysis. This study ultimately seeks to contribute to future studies on the lower respiratory tract in cancer patients with cytotoxic chemotherapy by establishing reliable control data.}, }
@article {pmid38025434, year = {2023}, author = {Hall, CV and Radford-Smith, G and Savage, E and Robinson, C and Cocchi, L and Moran, RJ}, title = {Brain signatures of chronic gut inflammation.}, journal = {Frontiers in psychiatry}, volume = {14}, number = {}, pages = {1250268}, doi = {10.3389/fpsyt.2023.1250268}, pmid = {38025434}, issn = {1664-0640}, abstract = {Gut inflammation is thought to modify brain activity and behaviour via modulation of the gut-brain axis. However, how relapsing and remitting exposure to peripheral inflammation over the natural history of inflammatory bowel disease (IBD) contributes to altered brain dynamics is poorly understood. Here, we used electroencephalography (EEG) to characterise changes in spontaneous spatiotemporal brain states in Crohn's Disease (CD) (n = 40) and Ulcerative Colitis (UC) (n = 30), compared to healthy individuals (n = 28). We first provide evidence of a significantly perturbed and heterogeneous microbial profile in CD, consistent with previous work showing enduring and long-standing dysbiosis in clinical remission. Results from our brain state assessment show that CD and UC exhibit alterations in the temporal properties of states implicating default-mode network, parietal, and visual regions, reflecting a shift in the predominance from externally to internally-oriented attentional modes. We investigated these dynamics at a finer sub-network resolution, showing a CD-specific and highly selective enhancement of connectivity between the insula and medial prefrontal cortex (mPFC), regions implicated in cognitive-interoceptive appraisal mechanisms. Alongside overall higher anxiety scores in CD, we also provide preliminary support to suggest that the strength of chronic interoceptive hyper-signalling in the brain co-occurs with disease duration. Together, our results demonstrate that a long-standing diagnosis of CD is, in itself, a key factor in determining the risk of developing altered brain network signatures.}, }
@article {pmid38025161, year = {2023}, author = {Chowdhary, A and Van Gelder, RN and Sundararajan, M}, title = {Methodologic Considerations for Studying the Ocular Surface Microbiome.}, journal = {Ophthalmology science}, volume = {3}, number = {4}, pages = {100408}, doi = {10.1016/j.xops.2023.100408}, pmid = {38025161}, issn = {2666-9145}, abstract = {UNLABELLED: The ocular surface microbiome, unlike that of the skin or gut, has not been well characterized. Culture experiments historically suggested a nearly sterile ocular surface, but initial application of molecular methods such as 16S ribosomal RNA and high-throughput sequencing demonstrated a surprisingly rich ocular surface microbiome. However, a major limitation in studying such a low-biomass niche is the potential for artifactual results when amplification-based techniques such as ribosomal polymerase chain reaction and shotgun sequencing are used. It will be essential to establish standards across the field for sample collection, positive and negative controls, and limitation of contamination in both the laboratory setting and computational analysis. New developments in ocular microbiome research, including the generation of reference reagents and fluoroscopic imaging techniques, provide improved means to validate sequencing results and to visualize complex interactions between host cells and bacteria. Through more thorough characterization of the ocular surface microbiome, the connections between a dysregulated surface and ophthalmic disease may be better understood.<br><br>FINANCIAL DISCLOSURES: Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.}, }
@article {pmid38024855, year = {2023}, author = {Mao, Z and Hui, H and Zhao, X and Xu, L and Qi, Y and Yin, L and Qu, L and Han, L and Peng, J}, title = {Protective effects of dioscin against Parkinson's disease via regulating bile acid metabolism through remodeling gut microbiome/GLP-1 signaling.}, journal = {Journal of pharmaceutical analysis}, volume = {13}, number = {10}, pages = {1153-1167}, doi = {10.1016/j.jpha.2023.06.007}, pmid = {38024855}, issn = {2214-0883}, abstract = {It is necessary to explore potent therapeutic agents via regulating gut microbiota and metabolism to combat Parkinson's disease (PD). Dioscin, a bioactive steroidal saponin, shows various activities. However, its effects and mechanisms against PD are limited. In this study, dioscin dramatically alleviated neuroinflammation and oxidative stress, and restored the disorders of mice induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). 16 S rDNA sequencing assay demonstrated that dioscin reversed MPTP-induced gut dysbiosis to decrease Firmicutes-to-Bacteroidetes ratio and the abundances of Enterococcus, Streptococcus, Bacteroides and Lactobacillus genera, which further inhibited bile salt hydrolase (BSH) activity and blocked bile acid (BA) deconjugation. Fecal microbiome transplantation test showed that the anti-PD effect of dioscin was gut microbiota-dependent. In addition, non-targeted fecal metabolomics assays revealed many differential metabolites in adjusting steroid biosynthesis and primary bile acid biosynthesis. Moreover, targeted bile acid metabolomics assay indicated that dioscin increased the levels of ursodeoxycholic acid, tauroursodeoxycholic acid, taurodeoxycholic acid and β-muricholic acid in feces and serum. In addition, ursodeoxycholic acid administration markedly improved the protective effects of dioscin against PD in mice. Mechanistic test indicated that dioscin significantly up-regulated the levels of takeda G protein-coupled receptor 5 (TGR5), glucagon-like peptide-1 receptor (GLP-1R), GLP-1, superoxide dismutase (SOD), and down-regulated NADPH oxidases 2 (NOX2) and nuclear factor-kappaB (NF-κB) levels. Our data indicated that dioscin ameliorated PD phenotype by restoring gut dysbiosis and regulating bile acid-mediated oxidative stress and neuroinflammation via targeting GLP-1 signal in MPTP-induced PD mice, suggesting that the compound should be considered as a prebiotic agent to treat PD in the future.}, }
@article {pmid38024851, year = {2023}, author = {Ravi, A and Marietta, EV and Alexander, JA and Murray, JA and Katzka, DA}, title = {H influenzae LPS colocalization with Toll-like receptor 4 in eosinophilic esophagitis.}, journal = {The journal of allergy and clinical immunology. Global}, volume = {2}, number = {4}, pages = {100151}, doi = {10.1016/j.jacig.2023.100151}, pmid = {38024851}, issn = {2772-8293}, abstract = {BACKGROUND: Patients with eosinophilic esophagitis (EoE) have a unique esophageal microbiome with increased presence of Haemophilus influenzae, but its role in the disease is unclear.<br><br>OBJECTIVE: Microbiome-derived bacterial LPS activation of Toll-like receptors (TLR) is a potential mechanism for inducing inflammation in other chronic inflammatory diseases, but it has not been studied in EoE. Our aim was therefore to study microbiome-derived bacterial LPS activation of TLRs in EoE.<br><br>METHODS: We studied 10 patients with active EoE, 9 patients with inactive EoE, and 10 control patients. Esophageal biopsy samples from the controls, patients with active EoE (>15 eosinophils/hpf), and patients with inactive EoE were immunostained for the presence of H influenzae LPS, presence of TLR4, and colocalization of LPS and TLR4. Staining intensity was measured by using confocal laser microscopy and scored on a scale from 0 to 3 as the average score assigned by 2 blinded observers.<br><br>RESULTS: H influenzae LPS was detected by positive staining in 20 of the 29 patients (69.0%), including 9 of the 10 patients with active EoE (90.0%), 8 of the 9 patients with inactive EoE (89.9%), and 3 of the 10 controls (30%); its level was greater in the patients with active EoE than in the controls (P&#xa0;= .063). TLR4 was detected by positive staining in 19 of the 29 patients (65.5%), including 9 of the 10 patients with active EoE (90.0%), 4 of the 9 patients with inactive EoE (44.4%), and 6 of the 10 controls (60.0%); its level was higher in the patients with active EoE than in those with inactive EoE (P&#xa0;= .096). The result of testing for colocalization of LPS and TLR4 was positive in 8 of 10 patients with active EoE (80.0%), 1 of 9 patients with inactive EoE (11.1%), and 1 of 10 control patients (10.0%), with greater colocalization of H influenzae LPS and TLR4 staining density in the samples from patients with active EoE than in the controls or the patients with inactive EoE (P&#xa0;= .009 and P&#xa0;= .018, respectively).<br><br>CONCLUSION: Esophageal microbiome-rich H influenzae LPS colocalizes to TLR4 in active EoE. These data lend further support to a role for the esophageal microbiome in modulating the activity of EoE.}, }
@article {pmid38024475, year = {2023}, author = {Zhao, W and Lei, J and Ke, S and Chen, Y and Xiao, J and Tang, Z and Wang, L and Ren, Y and Alnaggar, M and Qiu, H and Shi, W and Yin, L and Chen, Y}, title = {Fecal microbiota transplantation plus tislelizumab and fruquintinib in refractory microsatellite stable metastatic colorectal cancer: an open-label, single-arm, phase II trial (RENMIN-215).}, journal = {EClinicalMedicine}, volume = {66}, number = {}, pages = {102315}, doi = {10.1016/j.eclinm.2023.102315}, pmid = {38024475}, issn = {2589-5370}, abstract = {BACKGROUND: Immunotherapy has revolutionized the treatment of cancer. However, microsatellite stable (MSS) metastatic colorectal cancer (mCRC) shows a low response to PD-1 inhibitors. Antiangiogenic therapy can enhance anti-PD-1 efficacy, but it still cannot meet clinical needs. Increasing evidence supported a close relationship between gut microbiome and anti-PD-1 efficacy. This study aimed to explore the efficacy and safety of the combination of fecal microbiota transplantation (FMT) and tislelizumab and fruquintinib in refractory MSS mCRC.<br><br>METHODS: In the phase II trial, MSS mCRC patients were administered FMT plus tislelizumab and fruquintinib as a third-line or above treatment. The primary endpoint was progression-free survival (PFS). Secondary endpoints were overall survival (OS), objective response rate (ORR), disease control rate (DCR), duration of response (DoR), clinical benefit rate (CBR), safety and quality of life. Feces and peripheral blood were collected for exploratory biomarker analysis. This study is registered with Chictr.org.cn, identifier ChiCTR2100046768.<br><br>FINDINGS: From May 10, 2021 to January 17, 2022, 20 patients were enrolled. Median follow-up was 13.7 months. Median PFS was 9.6 months (95% CI 4.1-15.1). Median OS was 13.7 months (95% CI 9.3-17.7). Median DoR was 8.1 months (95% CI 1.7-10.6). ORR was 20% (95% CI 5.7-43.7). DCR was 95% (95% CI 75.1-99.9). CBR was 60% (95% CI 36.1-80.9). Nineteen patients (95%) experienced at least one treatment-related adverse event (TRAE). Six patients (30%) had grade 3-4 TRAEs, with the most common being albuminuria (10%), urine occult blood (10%), fecal occult blood (10%), hypertension (5%), hyperglycemia (5%), liver dysfunction (5%), hand-foot skin reaction (5%), and hypothyroidism (5%). No treatment-related deaths occurred. Responders had a high-abundance of Proteobacteria and Lachnospiraceae family and a low-abundance of Actinobacteriota and Bifidobacterium. The treatment did not change the structure of peripheral blood TCR repertoire. However, the expanded TCRs exhibited the characteristics of antigen-driven responses in responders.<br><br>INTERPRETATION: FMT plus tislelizumab and fruquintinib as third-line or above treatment showed improved survival and manageable safety in refractory MSS mCRC, suggesting a valuable new treatment option for this patient population.<br><br>FUNDING: This study was supported by the National Natural Science Foundation of China (82102954 to Wensi Zhao) and the Special Project of Central Government for Local Science and Technology Development of Hubei Province (ZYYD2020000169 to Yongshun Chen).}, }
@article {pmid38024360, year = {2023}, author = {Baek, GH and Kim, YJ and Lee, Y and Jung, SC and Seo, HW and Kim, JS}, title = {Prebiotic potential of green banana flour: impact on gut microbiota modulation and microbial metabolic activity in a murine model.}, journal = {Frontiers in nutrition}, volume = {10}, number = {}, pages = {1249358}, doi = {10.3389/fnut.2023.1249358}, pmid = {38024360}, issn = {2296-861X}, abstract = {INTRODUCTION: Green banana flour can be used as a prebiotic due to its ability to promote gut health and provide several health benefits. In this study, we investigated whether feeding mice green banana flour at different doses would alter intestinal microbiota composition.<br><br>METHODS: We fed C57BL/6N mice either a Low-dose (500 mg/kg/day) or High-dose (2000 mg/kg/day) of green banana flour daily for 3 weeks, and fecal samples were collected on days 0, 14, and 21 for microbiota analysis.<br><br>RESULTS: Our results showed that the composition of intestinal microbiota was significantly altered by day 21, regardless of the dose. Notably, the consumption of green banana flour increased the presence of beneficial bacteria, including Coriobacteriaceae_UCG-002, Turicibacter, Parasutterella, Gastranaerophilales_ge, and RF39_ge. These changes in the intestinal microorganisms were accompanied by increased biological processes such as amino acid biosynthesis and secondary metabolite biosynthesis. Conversely, the consumption of green banana flour resulted in a decrease in biological processes related to carbohydrate degradation, glycerol degradation, and similar functions.<br><br>DISCUSSION: These results emphasize the potential of green banana flour as a prebiotic that can benefit the gut microbiome.}, }
@article {pmid38024319, year = {2023}, author = {Wojciechowska, O and Costabile, A and Kujawska, M}, title = {The gut microbiome meets nanomaterials: exposure and interplay with graphene nanoparticles.}, journal = {Nanoscale advances}, volume = {5}, number = {23}, pages = {6349-6364}, doi = {10.1039/d3na00696d}, pmid = {38024319}, issn = {2516-0230}, abstract = {Graphene-based nanoparticles are widely applied in many technology and science sectors, raising concerns about potential health risks. Emerging evidence suggests that graphene-based nanomaterials may interact with microorganisms, both pathogens and commensal bacteria, that dwell in the gut. This review aims to demonstrate the current state of knowledge on the interplay between graphene nanomaterials and the gut microbiome. In this study, we briefly overview nanomaterials, their usage and the characteristics of graphene-based nanoparticles. We present and discuss experimental data from in vitro studies, screening tests on small animals and rodent experiments related to exposure and the effects of graphene nanoparticles on gut microbiota. With this in mind, we highlight the reported crosstalk between graphene nanostructures, the gut microbial community and the host immune system in order to shed light on the perspective to bear on the biological interactions. The studies show that graphene-based material exposure is dosage and time-dependent, and different derivatives present various effects on host bacteria cells. Moreover, the route of graphene exposure might influence a shift in the gut microbiota composition, including the alteration of functions and diversity and abundance of specific phyla or genera. However, the mechanism of graphene-based nanomaterials' influence on gut microbiota is poorly understood. Accordingly, this review emphasises the importance of studies needed to establish the most desirable synthesis methods, types of derivatives, properties, and safety aspects mainly related to the routes of exposure and dosages of graphene-based nanomaterials.}, }
@article {pmid38024144, year = {2023}, author = {Senaratne, NLM and Chong, CW and Yong, LS and Yoke, LF and Gopinath, D}, title = {Impact of waterpipe smoking on the salivary microbiome.}, journal = {Frontiers in oral health}, volume = {4}, number = {}, pages = {1275717}, doi = {10.3389/froh.2023.1275717}, pmid = {38024144}, issn = {2673-4842}, abstract = {BACKGROUND: While oral mirobial dysbiosis due to tobacco smoking has been studied thoroughly, there is limited data on the effect of waterpipe smoking on the oral microbiome. This study aims to compare the salivary microbiome between waterpipe smokers and non-smokers.<br><br>MATERIALS AND METHODS: Unstimulated saliva samples were collected from 60 participants, 30 smokers and 30 non-smokers in Kuala Lumpur and Klang Valley, Malaysia. DNA extraction was performed using the Qiagen DNA mini kit, and the 16S rRNA bacterial gene was amplified and sequenced using the Illumina MiSeq platform. Sequencing reads were processed using DADA2, and the alpha and beta diversity of the bacterial community was assessed. Significantly differentiated taxa were identified using LEfSe analysis, while differentially expressed pathways were identified using MaAsLin2.<br><br>RESULTS: A significant compositional change (beta diversity) was detected between the two groups (PERMANOVA P&#x2009;<&#x2009;0.05). Specifically, the levels of phylum Firmicutes and genus Streptococcus were elevated in smokers, whereas phylum Proteobacteria and genus Haemophilus were depleted compared to non-smokers. At the species level, Streptococcus oralis, Streptococcus salivarius, and Streptococcus gingivalis were enriched in smokers. We observed significant differences in the abundance of thirty-seven microbial metabolic pathways between waterpipe smokers and non-smokers. The microbial pathways enriched in smokers were those implicated in polymer degradation and amino acid metabolism.<br><br>CONCLUSION: The taxonomic and metabolic profile of the salivary microbiome in waterpipe smokers compared to healthy controls exhibited a paradigm shift, thus, implying an alteration in the homeostatic balance of the oral cavity posing unique challenges for oral health.}, }
@article {pmid38024036, year = {2023}, author = {Dewi, DAR and Perdiyana, A and Wiliantari, NM and Nadhira, F and Arkania, N and Salsabila, CA and Allun, CV and Allatib, A and Dewantara, K}, title = {Managing the Skin Microbiome as a New Bacteriotherapy for Inflammatory Atopic Dermatitis.}, journal = {Cureus}, volume = {15}, number = {11}, pages = {e48803}, doi = {10.7759/cureus.48803}, pmid = {38024036}, issn = {2168-8184}, abstract = {The microbiome, comprising various bacteria, assumes a significant role in the immune system's maturation and maintaining bodily homeostasis. Alterations in the microbial composition can contribute to the initiation and progression of inflammation. Recent studies reveal that changes in microbial composition and function, known as dysbiosis in the skin and gut, have been associated with altered immunological responses and skin barrier disruption. These changes are implicated in the development of several skin diseases, such as atopic dermatitis (AD). This review examines research demonstrating the potential of microbiome repair as a therapeutic approach to reduce the effect of inflammatory processes in the skin during atopic dermatitis. This way, corticosteroids in atopic dermatitis therapy can be reduced or even replaced with treatments focusing on controlling the skin microbiome. This study used scientific literature from recognized platforms, including PubMed, Scopus, Google Scholar, and ScienceDirect, covering publications from 2013 to 2023. The primary aim of this study was to assess the efficacy of skin microbiome management in treating atopic dermatitis. This study concludes that physicians must comprehensively understand the microbiome's involvement in atopic dermatitis, including its pathophysiological implications and its relevance to therapeutic interventions.}, }
@article {pmid38023904, year = {2023}, author = {Fu, X and Huang, Y and Fu, Q and Qiu, Y and Zhao, J and Li, J and Wu, X and Yang, Y and Liu, H and Yang, X and Chen, H}, title = {Critical transition of soil microbial diversity and composition triggered by plant rhizosphere effects.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1252821}, doi = {10.3389/fpls.2023.1252821}, pmid = {38023904}, issn = {1664-462X}, abstract = {Over the years, microbial community composition in the rhizosphere has been extensively studied as the most fascinating topic in microbial ecology. In general, plants affect soil microbiota through rhizodeposits and changes in abiotic conditions. However, a consensus on the response of microbiota traits to the rhizosphere and bulk soils in various ecosystems worldwide regarding community diversity and structure has not been reached yet. Here, we conducted a meta-analysis of 101 studies to investigate the microbial community changes between the rhizosphere and bulk soils across various plant species (maize, rice, vegetables, other crops, herbaceous, and woody plants). Our results showed that across all plant species, plant rhizosphere effects tended to reduce the rhizosphere soil pH, especially in neutral or slightly alkaline soils. Beta-diversity of bacterial community was significantly separated between into rhizosphere and bulk soils. Moreover, r-strategists and copiotrophs (e.g. Proteobacteria and Bacteroidetes) enriched by 24-27% in the rhizosphere across all plant species, while K-strategists and oligotrophic (e.g. Acidobacteria, Gemmatimonadete, Nitrospirae, and Planctomycetes) decreased by 15-42% in the rhizosphere. Actinobacteria, Firmicutes, and Chloroflexi are also depleted by in the plant rhizosphere compared with the bulk soil by 7-14%. The Actinobacteria exhibited consistently negative effect sizes across all plant species, except for maize and vegetables. In Firmicutes, both herbaceous and woody plants showed negative responses to rhizosphere effects, but those in maize and rice were contrarily enriched in the rhizosphere. With regards to Chloroflexi, apart from herbaceous plants showing a positive effect size, the plant rhizosphere effects were consistently negative across all other plant types. Verrucomicrobia exhibited a significantly positive effect size in maize, whereas herbaceous plants displayed a negative effect size in the rhizosphere. Overall, our meta-analysis exhibited significant changes in microbial community structure and diversity responding to the plant rhizosphere effects depending on plant species, further suggesting the importance of plant rhizosphere to environmental changes influencing plants and subsequently their controls over the rhizosphere microbiota related to nutrient cycling and soil health.}, }
@article {pmid38023867, year = {2023}, author = {Cardoni, M and Mercado-Blanco, J}, title = {Confronting stresses affecting olive cultivation from the holobiont perspective.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1261754}, doi = {10.3389/fpls.2023.1261754}, pmid = {38023867}, issn = {1664-462X}, abstract = {The holobiont concept has revolutionized our understanding of plant-associated microbiomes and their significance for the development, fitness, growth and resilience of their host plants. The olive tree holds an iconic status within the Mediterranean Basin. Innovative changes introduced in olive cropping systems, driven by the increasing demand of its derived products, are not only modifying the traditional landscape of this relevant commodity but may also imply that either traditional or emerging stresses can affect it in ways yet to be thoroughly investigated. Incomplete information is currently available about the impact of abiotic and biotic pressures on the olive holobiont, what includes the specific features of its associated microbiome in relation to the host's structural, chemical, genetic and physiological traits. This comprehensive review consolidates the existing knowledge about stress factors affecting olive cultivation and compiles the information available of the microbiota associated with different olive tissues and organs. We aim to offer, based on the existing evidence, an insightful perspective of diverse stressing factors that may disturb the structure, composition and network interactions of the olive-associated microbial communities, underscoring the importance to adopt a more holistic methodology. The identification of knowledge gaps emphasizes the need for multilevel research approaches and to consider the holobiont conceptual framework in future investigations. By doing so, more powerful tools to promote olive's health, productivity and resilience can be envisaged. These tools may assist in the designing of more sustainable agronomic practices and novel breeding strategies to effectively face evolving environmental challenges and the growing demand of high quality food products.}, }
@article {pmid38023855, year = {2023}, author = {Jia, J and Chen, L and Yu, W and Cai, S and Su, S and Xiao, X and Tang, X and Jiang, X and Chen, D and Fang, Y and Wang, J and Luo, X and Li, J and Huang, Y and Su, J}, title = {The novel nematicide chiricanine A suppresses Bursaphelenchus xylophilus pathogenicity in Pinus massoniana by inhibiting Aspergillus and its secondary metabolite, sterigmatocystin.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1257744}, doi = {10.3389/fpls.2023.1257744}, pmid = {38023855}, issn = {1664-462X}, abstract = {INTRODUCTION: Pine wilt disease (PWD) is responsible for extensive economic and ecological damage to Pinus spp. forests and plantations worldwide. PWD is caused by the pine wood nematode (PWN, Bursaphelenchus xylophilus) and transmitted into pine trees by a vector insect, the Japanese pine sawyer (JPS, Monochamus alternatus). Host infection by PWN will attract JPS to spawn, which leads to the co-existence of PWN and JPS within the host tree, an essential precondition for PWD outbreaks. Through the action of their metabolites, microbes can manipulate the co-existence of PWN and JPS, but our understanding on how key microorganisms engage in this process remains limited, which severely hinders the exploration and utilization of promising microbial resources in the prevention and control of PWD.<br><br>METHODS: In this study we investigated how the PWN-associated fungus Aspergillus promotes the co-existence of PWN and JPS in the host trees (Pinus massoniana) via its secondary metabolite, sterigmatocystin (ST), by taking a multi-omics approach (phenomics, transcriptomics, microbiome, and metabolomics).<br><br>RESULTS: We found that Aspergillus was able to promote PWN invasion and pathogenicity by increasing ST biosynthesis in the host plant, mainly by suppressing the accumulation of ROS (reactive oxygen species) in plant tissues that could counter PWN. Further, ST accumulation triggered the biosynthesis of VOC (volatile organic compounds) that attracts JPS and drives the coexistence of PWN and JPS in the host plant, thereby encouraging the local transmission of PWD. Meanwhile, we show that application of an Aspergillus inhibitor (chiricanine A treatment) results in the absence of Aspergillus and decreases the in vivo ST amount, thereby sharply restricting the PWN development in host. This further proved that Aspergillus is vital and sufficient for promoting PWD transmission.<br><br>DISCUSSION: Altogether, these results document, for the first time, how the function of Aspergillus and its metabolite ST is involved in the entire PWD transmission chain, in addition to providing a novel and long-term effective nematicide for better PWD control in the field.}, }
@article {pmid38023844, year = {2023}, author = {Shahid, I and Brunetto, G and Ricachenevsky, FK}, title = {Editorial: Capacity of the zinc mobilizing microbiome for climate-smart &amp; sustainable agriculture.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1323144}, doi = {10.3389/fpls.2023.1323144}, pmid = {38023844}, issn = {1664-462X}, }
@article {pmid38023837, year = {2023}, author = {Oldstone-Jackson, C and Huang, F and Bergelson, J}, title = {Microbe-associated molecular pattern recognition receptors have little effect on endophytic Arabidopsis thaliana microbiome assembly in the field.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1276472}, doi = {10.3389/fpls.2023.1276472}, pmid = {38023837}, issn = {1664-462X}, abstract = {Plant microbiome structure affects plant health and productivity. A limited subset of environmental microbes successfully establishes within plant tissues, but the forces underlying this selectivity remain poorly characterized. Transmembrane pattern recognition receptors (PRRs), used by plants to detect microbe-associated molecular patterns (MAMPs), are strong candidates for achieving this selectivity because PRRs can potentially interact with many members of the microbiome. Indeed, MAMPs found in many microbial taxa, including beneficials and commensals, can instigate a robust immune response that affects microbial growth. Surprisingly, we found that MAMP-detecting PRRs have little effect on endophytic bacterial and fungal microbiome structure in the field. We compared the microbiomes of four PRR knockout lines of Arabidopsis thaliana to wild-type plants in multiple tissue types over several developmental stages and detected only subtle shifts in fungal, but not bacterial, β-diversity in one of the four PRR mutants. In one developmental stage, lore mutants had slightly altered fungal β-diversity, indicating that LORE may be involved in plant-fungal interactions in addition to its known role in detecting certain bacterial lipids. No other effects of PRRs on α-diversity, microbiome variability, within-individual homogeneity, or microbial load were found. The general lack of effect suggests that individual MAMP-detecting PRRs are not critical in shaping the endophytic plant microbiome. Rather, we suggest that MAMP-detecting PRRs must either act in concert and/or are individually maintained through pleiotropic effects or interactions with coevolved mutualists or pathogens. Although unexpected, these results offer insights into the role of MAMP-detecting PRRs in plant-microbe interactions and help direct future efforts to uncover host genetic elements that control plant microbiome assembly.}, }
@article {pmid38023592, year = {2023}, author = {Yun, HM and Hyun, S}, title = {Role of gut commensal bacteria in juvenile developmental growth of the host: insights from Drosophila studies.}, journal = {Animal cells and systems}, volume = {27}, number = {1}, pages = {329-339}, doi = {10.1080/19768354.2023.2282726}, pmid = {38023592}, issn = {1976-8354}, abstract = {The gut microbiome plays a crucial role in maintaining health in a variety of organisms, from insects to humans. Further, beneficial symbiotic microbes are believed to contribute to improving the quality of life of the host. Drosophila is an optimal model for studying host-commensal microbe interactions because it allows for convenient manipulation of intestinal microbial composition. Fly microbiota has a simple taxonomic composition and can be cultivated and genetically tracked. This permits functional studies and analyses of the molecular mechanisms underlying their effects on host physiological processes. In this context, we briefly introduce the principle of juvenile developmental growth in Drosophila. Then, we discuss the current understanding of the molecular mechanisms underlying the effects of gut commensal bacteria, such as Lactiplantibacillus plantarum and Acetobacter pomorum, in the fly gut microbiome on Drosophila juvenile growth, including specific actions of gut hormones and metabolites in conserved cellular signaling systems, such as the insulin/insulin-like (IIS) and the target of rapamycin (TOR) pathways. Given the similarities in tissue function/structure, as well as the high conservation of physiological systems between Drosophila and mammals, findings from the Drosophila model system will have significant implications for understanding the mechanisms underlying the interaction between the host and the gut microbiome in metazoans.}, }
@article {pmid38023425, year = {2023}, author = {Arce-Cordero, JA and Liu, T and Monteiro, HF and Jeong, KC and Faciola, AP}, title = {Megasphaera elsdenii and Saccharomyces cerevisiae as direct fed microbials and their impact on ruminal microbiome during an acute acidosis challenge in continuous culture.}, journal = {Translational animal science}, volume = {7}, number = {1}, pages = {txad123}, doi = {10.1093/tas/txad123}, pmid = {38023425}, issn = {2573-2102}, abstract = {Our objective was to evaluate the effects of combinations of Saccharomyces cerevisiae and Megasphaera elsdenii as direct-fed microbials (DFM) on ruminal microbiome during an acute acidosis challenge in a continuous culture system. Treatments provided a DFM dose of 1 × 10[8] colony-forming unit (CFU)/mL, as follows: control (no DFM), YM1 (S. cerevisiae and M. elsdenii strain 1), YM2 (S. cerevisiae and M. elsdenii strain 2), and YMM (S. cerevisiae and half of the doses of M. elsdenii strains 1 and 2). We conducted four experimental periods of 11 d, which consisted of non-acidotic days (1 to 8) and acidotic challenge days (9 to 11) to establish acute ruminal acidosis conditions with a common basal diet containing 12% neutral detergent fiber and 58% starch. Treatments were applied from days 8 to 11, and samples of liquid and solid-associated bacteria were collected on days 9 to 11. Overall, 128 samples were analyzed by amplification of the V4 region of bacterial 16S rRNA, and data were analyzed with R and SAS for alpha and beta diversity, taxa relative abundance, and correlation of taxa abundance with propionate molar proportion. We observed a lower bacterial diversity (Shannon index, P = 0.02) when YM1 was added to the diet in comparison to the three other treatments. Moreover, compared to control, addition of YM1 to the diet increased relative abundance of phylum Proteobacteria (P = 0.05) and family Succinivibrioceae (P = 0.05) in the solid fraction and tended to increase abundance of family Succinivibrioceae (P = 0.10) and genus Succinivibrio (P = 0.09) in the liquid fraction. Correlation analysis indicated a positive association between propionate molar proportion and relative abundance of Proteobacteria (r = 0.36, P = 0.04) and Succinivibrioceae (r = 0.36, P = 0.05) in the solid fraction. The inclusion of YM1 in high-grain diets with a high starch content resulted in greater abundance of bacteria involved in succinate synthesis which may have provided the substrate for the greater propionate synthesis observed.}, }
@article {pmid38023381, year = {2023}, author = {Ji, Z and Lu, X and Xue, M and Fan, Y and Tian, J and Dong, L and Zhu, C and Wen, H and Jiang, M}, title = {The probiotic effects of host-associated Bacillus velezensis in diets for hybrid yellow catfish (Pelteobagrus fulvidraco ♀ × Pelteobagrus vachelli ♂).}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {15}, number = {}, pages = {114-125}, doi = {10.1016/j.aninu.2023.08.004}, pmid = {38023381}, issn = {2405-6383}, abstract = {This study was to evaluate the potential of a host-associated Bacillus velezensis as a probiotic for hybrid yellow catfish (Pelteobagrus fulvidraco ♀ × Pelteobagrus vachelli ♂). Diets (B0 to B5) containing 0, 0.90 × 10[8], 0.80 × 10[9], 0.85 × 10[10], 0.90 × 10[11], 0.83 × 10[12] CFU/kg B. velezensis YFI-E109 were fed to the fish with initial weight (3.07 ± 0.08 g) in a recirculating aquaculture system for six weeks with three replicates, respectively. Probiotic effects were analyzed based on growth, body composition, liver and gut morphology, gut microbiome, and liver metabolome. Analysis of the bacterial genome has shown that the most abundant genes in B. velezensis YFI-E109 were distributed in carbohydrate and amino acid metabolism. Fish in groups B3 and B4 had better growth performance, and higher intestinal amylase (AMS) and lipase (LPS) activities compared with other groups (P < 0.05). Fish in groups B0 and B5 showed significant liver damage, while this status improved in group B3. The liver malondialdehyde (MDA) content in group B3 was lower than that in other groups (P < 0.05). The abundance of Mycoplasma, Ralstonia and Acinetobacter was significantly reduced in B3 and B5 compared to B0. The amino acid and carbohydrate metabolism pathways were enriched in group B3 compared with group B0. In conclusion, dietary B. velezensis YFI-E109 supplementation has the potential to improve growth, liver metabolism, and liver and gut health, and reshape the gut microbiome of hybrid yellow catfish. Excessive B. velezensis YFI-E109 reduced the prebiotic effects. The recommended dietary supplementation of B. velezensis YFI-E109 is 0.31 × 10[10] to 0.77 × 10[11] CFU/kg for hybrid yellow catfish according to the quadratic regression method by plotting specific growth rate (SGR), feed conversion ratio (FCR), MDA and activities of AMS against dietary B. velezensis YFI-E109 levels.}, }
@article {pmid38023315, year = {2023}, author = {Awad, A and Pena, R}, title = {An improved method for extraction of soil fungal mycelium.}, journal = {MethodsX}, volume = {11}, number = {}, pages = {102477}, doi = {10.1016/j.mex.2023.102477}, pmid = {38023315}, issn = {2215-0161}, abstract = {Fungal mycelium is a major component of the soil microbiome. The soil hyphosphere represents a complex and dynamic niche for specific microorganisms, where multitrophic interactions occur, affecting ecosystem processes. However, extracting fungal mycelium from the soil to enable its taxonomical, chemical, and structural characterisation is challenging in the absence of a fast, efficient, and low-cost procedure. In this study, an old method (Bingle and Paul 1985), based on successive soil wet filtrations and density gradient centrifugation, was improved and tested in three different soil types (silty clay, silty clay loam, and loamy sand). The improved method reduced the number of filtrations by about five times and the centrifugation time from 40 min to 1 min. It avoided using any chemical substance which may impair further chemical analyses or DNA isolation and amplification. The method efficiency was about 50 % in the clay and 23 % in the sandy soils. However, a pre-step consisting of removing the fine-root fragments and other debris under the stereomicroscope may increase the method efficiency to more than 65 %, independent of the soil type.•A simple, efficient, and low-cost method suitable for extracting soil mycelium from a large number of samples.•The protocol includes successive soil wet filtrations and sucrose gradient centrifugation.•The method efficiency increases if the fine-root fragments and other debris are previously removed from the soil.}, }
@article {pmid38023290, year = {2023}, author = {Chorbińska, J and Krajewski, W and Nowak, &#x141; and Bardowska, K and Żebrowska-Różańska, P and Łaczmański, &#x141; and Pacyga-Prus, K and Górska, S and Małkiewicz, B and Szydełko, T}, title = {Is the Urinary and Gut Microbiome Associated With Bladder Cancer?.}, journal = {Clinical Medicine Insights. Oncology}, volume = {17}, number = {}, pages = {11795549231206796}, doi = {10.1177/11795549231206796}, pmid = {38023290}, issn = {1179-5549}, abstract = {BACKGROUND: Microbiome dysbiosis plays a role in the pathogenesis of many urological diseases, including bladder cancer (BC). The aim of the study was to compare the urinary and gut microbiota of patients with BC with a healthy control (HC) group.<br><br>METHODS: The study group included patients hospitalized in 2020 to 2021 with diagnosed BC and HC. Prior to the transurethral resection of bladder tumor, patients collected their urine and stool which was then subjected to 16S rRNA gene sequencing.<br><br>RESULTS: Overall, 25 patients were enrolled in the study: 18 in the BC group and 7 in the HC group. Analysis of the urine and stool microbiome showed no statistically significant differences between patients with BC and HC in alpha diversity, beta diversity, and difference in taxa relative abundance. Detailed analysis of urine and stool microbiome depending on patient- and tumor-related characteristics also showed no statistically significant differences in alpha diversity and beta diversity. Differences in abundance (ANCOM) were noted in both types of samples in patients with BC. In the urine test, genus Lactobacillus was more common in patients with a positive history of Bacillus Calmette-Gu&#xe9;rin (BCG) therapy, while genus Howardella and the strain Streptococcus anginosus were more common in women. In stool samples, abundance of phylum Desulfobacterota was most abundant in Grade G1 and least in G2. Class Alphaproteobacteria, order Rhodospirillales, order Flavobacteriales, and family Flavobacteriaceae were more common in women.<br><br>CONCLUSIONS: The microbiome of urine and stool of patients with BC does not differ significantly from that of HC; however, its composition in patients with BC varies according to the patient's sex.}, }
@article {pmid38023193, year = {2023}, author = {Thu, MS and Pongpirul, K}, title = {Response: Commentary: Human gut, breast, and oral microbiome in breast cancer: A systematic review and meta-analysis.}, journal = {Frontiers in oncology}, volume = {13}, number = {}, pages = {1279862}, doi = {10.3389/fonc.2023.1279862}, pmid = {38023193}, issn = {2234-943X}, }
@article {pmid38022878, year = {2023}, author = {Hadžić, E and Starcevic, A and Rupčić, T and Zucko, J and Čvrljak, T and Renko, I and Knjaz, D and Novak, D}, title = {Effects of Soluble Dietary Fibre on Exercise Performance and Perception of Fatigue in Young Basketball Players.}, journal = {Food technology and biotechnology}, volume = {61}, number = {3}, pages = {389-401}, doi = {10.17113/ftb.61.03.23.8124}, pmid = {38022878}, issn = {1330-9862}, abstract = {RESEARCH BACKGROUND: In this study, we investigated the effects of soluble dietary fibre on improving neuromuscular and cardiovascular endurance and perception of fatigue in a closely monitored group of basketball players. Prebiotics have been sidelined in sports nutrition and their effect on performance remains poorly investigated and understood.<br><br>EXPERIMENTAL APPROACH: Eighteen healthy male basketball players were divided into two groups; one received 17 g/day of soluble dietary fibre (Nutriose&#xae;) for four weeks and the other group received placebo. Their morphological characteristics, neuromuscular and cardiovascular endurance, and rating of perceived exertion according to the rating of perceived exertion (RPE) scale were assessed. Measurements were taken before supplementation and after four weeks of supplementation. Faecal samples were collected from all participants immediately before and after the supplementation period, their total DNA extracted and sent for amplicon sequencing.<br><br>RESULTS AND CONCLUSIONS: In this study, fibre had no statistically significant effect on the vertical-type explosive power, no statistically significant effect on sprint-type explosive power, nor on aerobic and anaerobic endurance in the experimental group. Soluble fibre had a statistically significant effect on reducing the rating of perceived exertion of basketball players during the competitive part of the season (RPE 7.27&#xb1;0.04 versus 8.82&#xb1;0.81). This was confirmed by two-way ANOVA with replication, which showed that within-group interaction (p=0.0193), before and after dietary intake (p=0.0049), and between-group interaction before and after dietary intake (p=0.0313) had a significant effect on the result. The overall conclusion of the study is that soluble dietary fibre supplementation does not improve neuromuscular and cardiovascular endurance over a 4-week period. However, fibre supplementation could have a significant effect on reducing the rating of perceived exertion, as shown by the statistics. Both amplicon sequencing and subsequent bioinformatics results suggest that this could be the result of the beneficial effect on the intestinal microbiota and its metabolites.<br><br>This work highlights the importance of prebiotics in sports nutrition. Dietary fibre has been a neglected component of sports nutrition. This study demonstrated a statistically significant positive effect on the perception of fatigue, highlighting the need for further studies in this direction.}, }
@article {pmid38022823, year = {2023}, author = {Shin, D and Kim, J and Lee, JH and Kim, JI and Oh, YM}, title = {Profiling of Microbial Landscape in Lung of Chronic Obstructive Pulmonary Disease Patients Using RNA Sequencing.}, journal = {International journal of chronic obstructive pulmonary disease}, volume = {18}, number = {}, pages = {2531-2542}, doi = {10.2147/COPD.S426260}, pmid = {38022823}, issn = {1178-2005}, abstract = {PURPOSE: The aim of the study was to use RNA sequencing (RNA-seq) data of lung from chronic obstructive pulmonary disease (COPD) patients to identify the bacteria that are most commonly detected. Additionally, the study sought to investigate the differences in these infections between normal lung tissues and those affected by COPD.<br><br>PATIENTS AND METHODS: We re-analyzed RNA-seq data of lung from 99 COPD patients and 93 non-COPD smokers to determine the extent to which the metagenomes differed between the two groups and to assess the reliability of the metagenomes. We used unmapped reads in the RNA-seq data that were not aligned to the human reference genome to identify more common infections in COPD patients.<br><br>RESULTS: We identified 18 bacteria that exhibited significant differences between the COPD and non-COPD smoker groups. Among these, Yersinia enterocolitica was found to be more than 30% more abundant in COPD. Additionally, we observed difference in detection rate based on smoking history. To ensure the accuracy of our findings and distinguish them from false positives, we double-check the metagenomic profile using Basic Local Alignment Search Tool (BLAST). We were able to identify and remove specific species that might have been misclassified as other species in Kraken2 but were actually Staphylococcus aureus, as identified by BLAST analysis.<br><br>CONCLUSION: This study highlighted the method of using unmapped reads, which were not typically used in sequencing data, to identify microorganisms present in patients with lung diseases such as COPD. This method expanded our understanding of the microbial landscape in COPD and provided insights into the potential role of microorganisms in disease development and progression.}, }
@article {pmid38022690, year = {2023}, author = {Meng, D and Ai, S and Spanos, M and Shi, X and Li, G and Cretoiu, D and Zhou, Q and Xiao, J}, title = {Exercise and microbiome: From big data to therapy.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {5434-5445}, doi = {10.1016/j.csbj.2023.10.034}, pmid = {38022690}, issn = {2001-0370}, abstract = {Exercise is a vital component in maintaining optimal health and serves as a prospective therapeutic intervention for various diseases. The human microbiome, comprised of trillions of microorganisms, plays a crucial role in overall health. Given the advancements in microbiome research, substantial databases have been created to decipher the functionality and mechanisms of the microbiome in health and disease contexts. This review presents an initial overview of microbiomics development and related databases, followed by an in-depth description of the multi-omics technologies for microbiome. It subsequently synthesizes the research pertaining to exercise-induced modifications of the microbiome and diseases that impact the microbiome. Finally, it highlights the potential therapeutic implications of an exercise-modulated microbiome in intestinal disease, obesity and diabetes, cardiovascular disease, and immune/inflammation-related diseases.}, }
@article {pmid38022618, year = {2023}, author = {Goyvaerts, C and Engeland, CE and Van der Jeught, K}, title = {Editorial: Rising stars in cancer immunity and immunotherapy 2022.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1326374}, doi = {10.3389/fimmu.2023.1326374}, pmid = {38022618}, issn = {1664-3224}, }
@article {pmid38022592, year = {2023}, author = {Alizadeh, M and Shojadoost, B and Boodhoo, N and Raj, S and Sharif, S}, title = {Molecular and cellular characterization of immunity conferred by lactobacilli against necrotic enteritis in chickens.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1301980}, doi = {10.3389/fimmu.2023.1301980}, pmid = {38022592}, issn = {1664-3224}, abstract = {Necrotic enteritis is an important enteric disease of poultry that can be controlled with in-feed antibiotics. However, with the concerns over antimicrobial resistance, there is an increased interest in the use of alternatives. Probiotics are one of the alternatives that have gained considerable attention due to their antimicrobial and immunomodulatory activities. Therefore, in the present study, we evaluated the effects of two different Lactobacillus species alone or as a cocktail on prevention of necrotic enteritis. Day-old male broiler chickens were divided into five groups and on days 1, 8, 15, and 22, birds in groups 2 and 3 received 1×10[8] colony forming units (CFU) of L. johnsonii and L. reuteri, respectively. Group 4 received probiotic cocktails containing both bacteria (10[8] CFU/bird) and the negative and positive control groups did not receive any lactobacilli. Starting on day 23 post-hatch, birds in all groups (except the negative control group) were orally challenged twice per day with 3×10[8] CFU of a pathogenic C. perfringens strain for 3 days. Tissue and cecal samples were collected before and after challenge to assess gene expression, lymphocyte subsets determination, and microbiome analysis. On day 26 of age, lesion scoring was performed. The results demonstrated that the group that received the lactobacilli cocktail had significantly reduced lesion scores compared to the positive control group. In addition, the expression of interleukin (IL)-12 in the jejunum and CXC motif chemokine ligand 8 (CXCL8), IL-13, and IL-17 in the ileum were downregulated in the group that received the lactobacilli cocktail when compared to the positive control. Treating chickens with the lactobacilli cocktail prior to challenge enhanced the percentage of CD3[-]CD8[+] cells and Bu-1[+]IgY[+] B cells in the ileum and increased the frequency of monocyte/macrophages, CD3[-]CD8[+] cells, Bu-1[+]IgM[+], and Bu-1[+]IgY[+] B cells in the jejunum. Treatment with the lactobacilli cocktail reduced the relative expression of Gamma-Protobacteria and Firmicutes compared to the positive control group. In conclusion, the results presented here suggest that treatment with the lactobacilli cocktail containing L. johnsonii and L. reuteri reduced necrotic enteritis lesions in the small intestine of chickens, possibly through the modulation of immune responses.}, }
@article {pmid38022583, year = {2023}, author = {Liu, X and van Beek, N and Cepic, A and Andreani, NA and Chung, CJ and Hermes, BM and Yilmaz, K and Benoit, S and Drenovska, K and Gerdes, S and Gläser, R and Goebeler, M and Günther, C and von Georg, A and Hammers, CM and Holtsche, MM and Hübner, F and Kiritsi, D and Schauer, F and Linnenmann, B and Huilaja, L and Tasanen-Määttä, K and Vassileva, S and Zillikens, D and Sadik, CD and Schmidt, E and Ibrahim, S and Baines, JF}, title = {The gut microbiome in bullous pemphigoid: implications of the gut-skin axis for disease susceptibility.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1212551}, doi = {10.3389/fimmu.2023.1212551}, pmid = {38022583}, issn = {1664-3224}, abstract = {Bullous pemphigoid (BP) is an autoimmune blistering disease that primarily affects the elderly. An altered skin microbiota in BP was recently revealed. Accumulating evidence points toward a link between the gut microbiota and skin diseases; however, the gut microbiota composition of BP patients remains largely underexplored, with only one pilot study to date, with a very limited sample size and no functional profiling of gut microbiota. To thoroughly investigate the composition and function of the gut microbiota in BP patients, and explore possible links between skin conditions and gut microbiota, we here investigated the gut microbiota of 66 patients (81.8% firstly diagnosed) suffering from BP and 66 age-, sex-, and study center-matched controls (CL) with non-inflammatory skin diseases (132 total participants), using 16S rRNA gene and shotgun sequencing data. Decreased alpha-diversity and an overall altered gut microbial community is observed in BP patients. Similar trends are observed in subclassifications of BP patients, including first diagnoses and relapsed cases. Furthermore, we observe a set of BP disease-associated gut microbial features, including reduced Faecalibacterium prausnitzii and greater abundance of pathways related to gamma-aminobutyric acid (GABA) metabolism in BP patients. Interestingly, F. prausnitzii is a well-known microbiomarker of inflammatory diseases, which has been reported to be reduced in the gut microbiome of atopic dermatitis and psoriasis patients. Moreover, GABA plays multiple roles in maintaining skin health, including the inhibition of itching by acting as a neurotransmitter, attenuating skin lesions by balancing Th1 and Th2 levels, and maintaining skin elasticity by increasing the expression of type I collagen. These findings thus suggest that gut microbiota alterations present in BP may play a role in the disease, and certain key microbes and functions may contribute to the link between gut dysbiosis and BP disease activity. Further studies to investigate the underlying mechanisms of the gut-skin interaction are thus clearly warranted, which could aid in the development of potential therapeutic interventions.}, }
@article {pmid38022571, year = {2023}, author = {Liu, X and Wang, X and Zhang, P and Fang, Y and Liu, Y and Ding, Y and Zhang, W}, title = {Intestinal homeostasis in the gut-lung-kidney axis: a prospective therapeutic target in immune-related chronic kidney diseases.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1266792}, doi = {10.3389/fimmu.2023.1266792}, pmid = {38022571}, issn = {1664-3224}, abstract = {In recent years, the role of intestinal homeostasis in health has received increasing interest, significantly improving our understanding of the complex pathophysiological interactions of the gut with other organs. Microbiota dysbiosis, impaired intestinal barrier, and aberrant intestinal immunity appear to contribute to the pathogenesis of immune-related chronic kidney diseases (CKD). Meanwhile, the relationship between the pathological changes in the respiratory tract (e.g., infection, fibrosis, granuloma) and immune-related CKD cannot be ignored. The present review aimed to elucidate the new underlying mechanism of immune-related CKD. The lungs may affect kidney function through intestinal mediation. Communication is believed to exist between the gut and lung microbiota across long physiological distances. Following the inhalation of various pathogenic factors (e.g., particulate matter 2.5 mum or less in diameter, pathogen) in the air through the mouth and nose, considering the anatomical connection between the nasopharynx and lungs, gut microbiome regulates oxidative stress and inflammatory states in the lungs and kidneys. Meanwhile, the intestine participates in the differentiation of T cells and promotes the migration of various immune cells to specific organs. This better explain the occurrence and progression of CKD caused by upper respiratory tract precursor infection and suggests the relationship between the lungs and kidney complications in some autoimmune diseases (e.g., anti-neutrophil cytoplasm antibodies -associated vasculitis, systemic lupus erythematosus). CKD can also affect the progression of lung diseases (e.g., acute respiratory distress syndrome and chronic obstructive pulmonary disease). We conclude that damage to the gut barrier appears to contribute to the development of immune-related CKD through gut-lung-kidney interplay, leading us to establish the gut-lung-kidney axis hypothesis. Further, we discuss possible therapeutic interventions and targets. For example, using prebiotics, probiotics, and laxatives (e.g., Rhubarb officinale) to regulate the gut ecology to alleviate oxidative stress, as well as improve the local immune system of the intestine and immune communication with the lungs and kidneys.}, }
@article {pmid38022530, year = {2023}, author = {Vietsch, EE and Latifi, D and Verheij, M and van der Oost, EWA and de Wilde, RF and Haen, R and van den Boom, AL and Koerkamp, BG and Doornebosch, PG and van Verschuer, VMT and Ooms, AHAG and Mohammad, F and Willemsen, M and Aerts, JGJV and Krog, RT and de Miranda, NFCC and van den Bosch, TPP and Mueller, YM and Katsikis, PD and van Eijck, CHJ}, title = {B cell immune profiles in dysbiotic vermiform appendixes of pancreatic cancer patients.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1230306}, doi = {10.3389/fimmu.2023.1230306}, pmid = {38022530}, issn = {1664-3224}, abstract = {Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest solid tumors and is resistant to immunotherapy. B cells play an essential role in PDAC progression and immune responses, both locally and systemically. Moreover, increasing evidence suggests that microbial compositions inside the tumor, as well as in the oral cavity and the gut, are important factors in shaping the PDAC immune landscape. However, the gut-associated lymphoid tissue (GALT) has not previously been explored in PDAC patients. In this study, we analyzed healthy vermiform appendix (VA) from 20 patients with PDAC and 32 patients with colon diseases by gene expression immune profiling, flow cytometry analysis, and microbiome sequencing. We show that the VA GALT of PDAC patients exhibits markers of increased inflammation and cytotoxic cell activity. In contrast, B cell function is decreased in PDAC VA GALT based on gene expression profiling; B cells express significantly fewer MHC class II surface receptors, whereas plasma cells express the immune checkpoint molecule HLA-G. Additionally, the vermiform appendix microbiome of PDAC patients is enriched with Klebsiella pneumoniae, Bifidobacterium animalis, and Adlercreutzia equolifaciens, while certain commensals are depleted. Our findings may suggest impaired B cell function within the GALT of PDAC patients, which could potentially be linked to microbial dysbiosis. Additional investigations are imperative to validate our observations and explore these potential targets of future therapies.}, }
@article {pmid38022505, year = {2023}, author = {Lawal, SA and Voisin, A and Olof, H and Bording-Jorgensen, M and Armstrong, H}, title = {Diversity of the microbiota communities found in the various regions of the intestinal tract in healthy individuals and inflammatory bowel diseases.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1242242}, doi = {10.3389/fimmu.2023.1242242}, pmid = {38022505}, issn = {1664-3224}, abstract = {The severe and chronic inflammatory bowel diseases (IBD), Crohn disease and ulcerative colitis, are characterized by persistent inflammation and gut damage. There is an increasing recognition that the gut microbiota plays a pivotal role in IBD development and progression. However, studies of the complete microbiota composition (bacteria, fungi, viruses) from precise locations within the gut remain limited. In particular, studies have focused primarily on the bacteriome, with available methods limiting evaluation of the mycobiome (fungi) and virome (virus). Furthermore, while the different segments of the small and large intestine display different functions (e.g., digestion, absorption, fermentation) and varying microenvironment features (e.g., pH, metabolites), little is known about the biogeography of the microbiota in different segments of the intestinal tract or how this differs in IBD. Here, we highlight evidence of the differing microbiota communities of the intestinal sub-organs in healthy and IBD, along with method summaries to improve future studies.}, }
@article {pmid38022043, year = {2023}, author = {Kaliamoorthy, S and Priya Sayeeram, S and SundarRaj, S and Balakrishnan, J and Nagarajan, M and Samidorai, A}, title = {Investigating the Association Between Fusobacterium nucleatum and Oral Squamous Cell Carcinoma: A Pilot Case-Control Study on Tissue Samples.}, journal = {Cureus}, volume = {15}, number = {10}, pages = {e47238}, doi = {10.7759/cureus.47238}, pmid = {38022043}, issn = {2168-8184}, abstract = {Background Fusobacterium nucleatum (F. nucleatum) has been increasingly linked to oral squamous cell carcinoma (OSCC), prompting this study to explore its presence using polymerase chain reaction (PCR) and evaluate its clinical significance. Methods In this pilot case-control study, 12 OSCC tissue samples and 12 non-cancerous oral mucosal tissue samples were analyzed. Total RNA extraction and complementary DNA (cDNA) synthesis were performed using Trizol-based methods, followed by PCR amplification and gel electrophoresis. The clinical characteristics of participants and PCR results were recorded. Results Among the OSCC tissue samples, three out of 12 tested positive for F. nucleatum, while none of the control samples showed its presence. The detection rate of F. nucleatum in OSCC was 25%. Gel analysis confirmed specific amplicon amplification, and ImageJ software enabled copy number quantification. Discussion Our findings support previous research indicating a potential association between F. nucleatum and OSCC. Understanding the etiological significance of F. nucleatum in OSCC has clinical implications, including early detection, risk stratification, and prognostication. However, the limited sample size and the need for further research to elucidate underlying mechanisms are acknowledged. Conclusion This pilot study provides initial evidence of F. nucleatum's presence in a subset of OSCC samples, supporting its potential association with oral cancer. Detecting F. nucleatum in OSCC tissues holds promise for future research and clinical applications as a diagnostic and prognostic biomarker. Understanding its role in oral carcinogenesis will facilitate the development of targeted therapeutic strategies. Larger studies are warranted to validate these findings and investigate the precise mechanisms involved.}, }
@article {pmid38021696, year = {2023}, author = {Algrafi, AS and Jamal, AA and Ismaeel, DM}, title = {Microbiota as a New Target in Cancer Pathogenesis and Treatment.}, journal = {Cureus}, volume = {15}, number = {10}, pages = {e47072}, doi = {10.7759/cureus.47072}, pmid = {38021696}, issn = {2168-8184}, abstract = {The microbial ecosystem of humans is an integral part of human health and disease. A significant percentage of tumors worldwide are thought to be microbially induced. The relationship between cancer and microbes is complex. In this article review, we aim to give an overview of human microbiota and its role in carcinogenesis, emphasize the relation between microbiota and cancer immunity, and highlight its role in the future of cancer therapy. The term microbiota refers to the collection of microorganisms that are located in an individual, whereas the total genome of these microorganisms is referred to as the microbiome. The microbiota in humans has many physiological functions. The microbiota within the gut lumen has a profound effect on the local and systemic immune system. The immune system can change the gut microbiota. Microbiota may induce carcinogenesis by several mechanisms. It also affects tumor progression. Thus, microbiota modulation may aid in the prevention and treatment of cancer. Intentionally introducing microorganisms into the oncological patient is assumed to mobilize the immune system to become able to, at least, limit the development of cancer. Microbes are used as vectors which are carriers of particular antineoplastic agents that reduce the side effects of chemotherapy. Inflammation and tumor microenvironment play an essential role in promoting chemo-resistance. There is now considerable evidence, both in humans as well as in laboratory animals, that the commensal microbiota has important effects on carcinogenesis, tumor growth, and therapy response.}, }
@article {pmid38021670, year = {2023}, author = {Sharma, N and Chakole, S and Wandile, B}, title = {Uncovering the Cardiovascular Threat: A Comprehensive Examination of Liver Fibrosis and Subclinical Atherosclerosis in Non-alcoholic Fatty Liver Disease.}, journal = {Cureus}, volume = {15}, number = {10}, pages = {e46946}, doi = {10.7759/cureus.46946}, pmid = {38021670}, issn = {2168-8184}, abstract = {Non-alcoholic fatty liver disease (NAFLD) has emerged as a global epidemic intricately linked to the rising tide of obesity and metabolic syndrome. This comprehensive review delves into the complex web of relationships between NAFLD, liver fibrosis, and subclinical atherosclerosis, shedding light on their interplay, shared risk factors, and clinical implications. NAFLD encompasses a spectrum of liver conditions, from the benign non-alcoholic fatty liver (NAFL) to the more severe non-alcoholic steatohepatitis (NASH), characterized by inflammation and hepatocellular injury. Central to the discussion is the insidious development of liver fibrosis, the ominous harbinger of progressive liver damage, cirrhosis, and hepatocellular carcinoma. The increasing prevalence of NAFLD, now affecting a quarter of the global population, poses a significant public health challenge. Its association with obesity, insulin resistance, and metabolic syndrome highlights the multifactorial nature of this disease. However, NAFLD's repercussions extend beyond the liver. This review unveils a potent connection between NAFLD and subclinical atherosclerosis, the early precursor to cardiovascular disease. Individuals with NAFLD face an elevated risk of atherosclerosis, even without traditional cardiovascular risk factors. The intricate link between these two conditions is illuminated through shared pathophysiological pathways, including systemic inflammation, insulin resistance, and dyslipidemia. Understanding the interplay between liver fibrosis and subclinical atherosclerosis has profound clinical implications. Patients with advanced fibrosis or cirrhosis are not only at risk of liver-related complications but also of cardiovascular events. This necessitates a holistic approach to patient care, with lifestyle modifications and pharmacological interventions simultaneously managing both conditions. Physicians must prioritize early detection and collaborate across disciplines to provide comprehensive care. Looking ahead, the future holds promising avenues of research. Emerging areas include genetics and precision medicine, microbiome research, and epigenetics, which may unveil new therapeutic targets. Innovations in diagnostics and therapeutics, such as non-invasive biomarkers and combination therapies, offer hope for more effective management. Long-term outcomes and survivorship research will provide insights into the lasting impact of interventions. In conclusion, this review underscores the imperative of addressing liver fibrosis and atherosclerosis in the context of NAFLD. It is a call to action for healthcare professionals, researchers, and policymakers to work collaboratively, promote early detection, and advance our understanding of these interconnected conditions. By doing so, we can enhance patient outcomes and chart a course toward a healthier future for those grappling with NAFLD and its intricate web of consequences.}, }
@article {pmid38021562, year = {2023}, author = {Antony, MA and Patel, S and Verma, V and Kant, R}, title = {The Role of Gut Microbiome Supplementation in COVID-19 Management.}, journal = {Cureus}, volume = {15}, number = {10}, pages = {e46960}, doi = {10.7759/cureus.46960}, pmid = {38021562}, issn = {2168-8184}, abstract = {COVID-19, which is caused by the RNA virus, SARS-CoV-2, mainly affects the respiratory system and has a varied clinical presentation. However, several studies have shown that COVID-19 can also affect the gastrointestinal (GI) system. Patients can experience various GI symptoms, such as vomiting and diarrhea, and the virus has been detected in the stool samples of patients hospitalized with COVID-19. There have also been rare reports of COVID-19 presenting with isolated GI symptoms and lack of respiratory symptoms, and the virus has also been detected for prolonged periods in the fecal samples of COVID-19 patients. Major alterations in the gut microbiome in the form of depletion of beneficial organisms and an abundance of pathogenic organisms have been reported in the fecal samples of hospitalized COVID-19 patients. Although the US FDA has approved several drugs to manage COVID-19, their efficacy remains modest. So, there is a constant ongoing effort to investigate novel treatment options for COVID-19. Health supplements like probiotics, prebiotics, postbiotics, and synbiotics have been popularly known for their various health benefits. In this review, we have summarized the current literature, which shows the potential benefit of these health supplements to mitigate and/or prevent the clinical presentation of COVID-19.}, }
@article {pmid38021395, year = {2023}, author = {Mohsen Hammad, DB and Abdulazeez Alhamad, O and Mahdy Obiad Khzal, A and Mahdi Muslim Alameedy, F}, title = {Molecular Characterisation of Blood Microbiome in Patients with Ankylosing Spondylitis and Healthy Controls.}, journal = {Medical journal of the Islamic Republic of Iran}, volume = {37}, number = {}, pages = {84}, doi = {10.47176/mjiri.37.84}, pmid = {38021395}, issn = {1016-1430}, abstract = {BACKGROUND: In human and animal studies, ankylosing spondylitis (AS) has been increasingly linked to changes in the microbial inhabitants in the human body (microbiome). These studies have primarily now concentrated on the microbial communities that live in the gastrointestinal tract. However, evidence suggests that various molecular techniques can be used to detect microbial DNA in blood circulation. This DNA might be an unknown reservoir of biomarkers with the potential to track alterations in the microbiomes of remote locations, such as the gut. To this end, we compared the presence and identity of microbial DNA in blood samples taken from ankylosing spondylitis patients to healthy control subjects by amplifying and sequencing the bacterial 16S rRNA variable region four.<br><br>METHODS: The study's design is a case study based on the presence and identity of bacterial DNA in the blood of Ankylosing spondylitis (AS) patients (n = 10) and healthy control subjects (n = 10) was investigated by amplifying and sequencing the bacterial 16S rRNA gene. Blood concentrations of the cytokines TNF alpha, IL-17A, and IL-23 were determined by the Human Magnetic Luminex Screening, and data were analysed using an Unpaired T-test.<br><br>RESULTS: Using PCR amplification, 8 of 10 AS patients (80%) and 8 of 10 healthy control samples (80%) had microbial 16S rRNA in their blood. At the phylum level, Proteobacteria (Control = 48.5%, AS = 52%), Firmicutes (Control = 27.8%, AS = 26.1%), Actinobacteria (Control = 15.4%, AS = 10.7%), and Bacteroidetes (Control = 6.5%, AS = 10%) dominated the blood microbiome. A two-tailed Mann-Whitney test found that Ankylosing Spondylitis was associated with significantly elevated Bacteroides (P < 0.05), Prevotella (P < 0.001), and Micrococcus (P < 0.01), and significantly reduced levels of Corynebacterium 1 (P < 0.001), Gemella (P < 0.01), and Alloprevotella (P < 0.05), compared to healthy controls. Additionally, it was shown that the presence of the Prevotella genus was highly positively correlated with higher levels of TNF-alpha (P < 0.05; r = 0.8) in AS patients' blood.<br><br>CONCLUSION: This article reveals that a blood microbiome exists in healthy individuals and identifies particular taxa modulated in disease. These blood-derived signatures indicate that this field needs more research and may be helpful as disease biomarkers.}, }
@article {pmid38021257, year = {2023}, author = {Chen, G and Yuan, Y and Tang, S and Yang, Z and Wu, Q and Liang, Z and Chen, S and Li, W and Lv, X and Ni, L}, title = {Comparative analysis of microbial communities and volatile flavor components in the brewing of Hongqu rice wines fermented with different starters.}, journal = {Current research in food science}, volume = {7}, number = {}, pages = {100628}, doi = {10.1016/j.crfs.2023.100628}, pmid = {38021257}, issn = {2665-9271}, abstract = {As one of the quintessential representatives of Chinese rice wine, Hongqu rice wine is brewed with glutinous rice as the main raw material and Hongqu (Gutian Qu or Wuyi Qu) as the fermentation starter. The present study aimed to investigate the impact of Hongqu on the volatile compositions and the microbial communities in the traditional production of Gutian Hongqu rice wine (GT) and Wuyi Hongqu rice wine (WY). Through the OPLS-DA analysis, 3-methylbutan-1-ol, isobutanol, ethyl lactate, ethyl acetate, octanoic acid, diethyl succinate, phenylethyl alcohol, hexanoic acid and n-decanoic acid were identified as the characteristic volatile flavor components between GT and WY. Microbiome analysis revealed significant enrichments of Lactobacillus, Pediococcus, Aspergillus and Hyphopichia in WY brewing, whereas Monascus, Saccharomyces, Pantoea, and Burkholderia-Caballeronia-Paraburkholderia were significantly enriched in GT brewing. Additionally, correlation analysis showed that Saccharomyces, Lactobacillus, Weissella and Pediococcus were significantly positively correlated wih most characteristic volatile components. Conversely, Picha, Monascus, Franconibacter and Kosakonia showed significant negative correlations with most of the characteristic volatile components. Furthermore, bioinformatical analysis indicated that the gene abundances for enzymes including glucan 1,4-alpha-glucosidase, carboxylesterase, alcohol dehydrogenase, dihydroxy-acid dehydratase and branched-chain-amino-acid transaminase were significantly higher in WY compared to GT. This finding explains the higher content of higher alcohols and characteristic esters in WY relative to GT. Collectively, this study provides a theoretical basis for improving the flavor profile of Hongqu rice wine and establishing a solid scientific foundation for the sustainable development of Hongqu rice wine industry.}, }
@article {pmid38020871, year = {2023}, author = {Li, D and Xia, W and Cui, X and Zhao, M and Huang, K and Wang, X and Shen, J and Chen, H and Zhu, L}, title = {The putatively high-altitude adaptation of macaque monkeys: Evidence from the fecal metabolome and gut microbiome.}, journal = {Evolutionary applications}, volume = {16}, number = {10}, pages = {1708-1720}, doi = {10.1111/eva.13595}, pmid = {38020871}, issn = {1752-4571}, abstract = {Animals living in high-altitude environments, such as the Tibetan Plateau, must face harsh environmental conditions (e.g., hypoxia, cold, and strong UV radiation). These animals' physiological adaptations (e.g., increased red cell production and turnover rate) might also be associated with the gut microbial response. Bilirubin is a component of red blood cell turnover or destruction and is excreted into the intestine and reduced to urobilinoids and/or urobilinogen by gut bacteria. Here, we found that the feces of macaques living in high-altitude regions look significantly browner (with a high concentration of stercobilin, a component from urobilinoids) than those living in low-altitude regions. We also found that gut microbes involved in urobilinogen reduction (e.g., beta-glucuronidase) were enriched in the high-altitude mammal population compared to the low-altitude population. Moreover, the spatial-temporal change in gut microbial function was more profound in the low-altitude macaques than in the high-altitude population, which might be attributed to profound changes in food resources in the low-altitude regions. Therefore, we conclude that a high-altitude environment's stress influences living animals and their symbiotic microbiota.}, }
@article {pmid38020771, year = {2023}, author = {Lee, EH and Kim, GH and Park, HK and Kang, HJ and Park, YK and Lee, HA and Hong, CH and Moon, SY and Kang, W and Oh, HS and Yoon, HJ and Choi, SH and Jeong, JH}, title = {Effects of the multidomain intervention with nutritional supplements on cognition and gut microbiome in early symptomatic Alzheimer's disease: a randomized controlled trial.}, journal = {Frontiers in aging neuroscience}, volume = {15}, number = {}, pages = {1266955}, doi = {10.3389/fnagi.2023.1266955}, pmid = {38020771}, issn = {1663-4365}, abstract = {BACKGROUND: The SoUth Korean study to PrEvent cognitive impaiRment and protect BRAIN health through lifestyle intervention in at-risk elderly people (SUPERBRAIN) is a part of the World-Wide Finnish Geriatric Intervention Study to Prevent Cognitive Impairment and Disability (WW-FINGERS) network. This study aimed to demonstrate the effects of the SUPERBRAIN-based multidomain intervention with nutritional supplements in amyloid positive emission tomography (PET) proven early symptomatic Alzheimer's disease patients.<br><br>METHODS: Forty-six participants who were diagnosed with mild cognitive impairment or mild dementia and were positive in the amyloid PET study randomized into three groups: group A, the multidomain intervention with nutritional supplements; group B, nutritional supplements only; and a control group. The primary outcome was a change in the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) total scale index score after an 8-week intervention. Secondary outcomes, including gut microbiome data, were also analyzed.<br><br>RESULTS: The RBANS total scale index score improved significantly in group A compared with group B (p&#x2009;<&#x2009;0.032) and compared with the control group (p&#x2009;<&#x2009;0.001). After intervention, beta diversity of the gut microbiome between group A and the control group increased, and patients in group A were more enriched with Bifidobacterium.<br><br>CONCLUSION: SUPERBRAIN-based multidomain intervention with nutritional supplements improves cognition and gut microbiota in patients with early symptomatic Alzheimer's disease who were amyloid-positive by PET.}, }
@article {pmid38020719, year = {2023}, author = {Lin, K and Dong, C and Zhao, B and Zhou, B and Yang, L}, title = {Glucagon-like peptide-1 receptor agonist regulates fat browning by altering the gut microbiota and ceramide metabolism.}, journal = {MedComm}, volume = {4}, number = {6}, pages = {e416}, doi = {10.1002/mco2.416}, pmid = {38020719}, issn = {2688-2663}, abstract = {Studies have shown that antidiabetic drugs can alter the gut microbiota. The hypoglycemic effects of the drugs can be attributed in part to certain species in the gut microbiome that help the drugs work more effectively. In addition, increasing energy expenditure via the induction of adipose tissue browning has become an appealing strategy to treat obesity and associated metabolic complications. Currently, glucagon-like peptide-1 receptor agonist (GLP-1 RA) treatment for metabolic disorders such as obesity and type 2 diabetes has been widely studied. To determine the mechanism of a long-acting GLP-1 RA affects adipose tissue browning and the gut microbiome, we treated high-fat diet mice with GLP-1 RA and demonstrated that the drug can regulate adipose tissue browning. 16S rRNA and untargeted metabolomics assays suggested that it increased the abundance of bacterium Lactobacillus reuteri and decreased serum ceramide levels in mice. L. reuteri was negatively correlated with ceramide. We found that the mechanism of ceramide decline was alkaline ceramidase 2 (Acer2) overexpression. Moreover, L. reuteri can play a therapeutic synergistic role with GLP-1 RA, suggesting that gut microbiota can be used as a part of the treatment of diabetes.}, }
@article {pmid38020524, year = {2023}, author = {Liss, MA and Reveles, KR and Tipton, CD and Gelfond, J and Tseng, T}, title = {Comparative Effectiveness Randomized Clinical Trial Using Next-generation Microbial Sequencing to Direct Prophylactic Antibiotic Choice Before Urologic Stone Lithotripsy Using an Interprofessional Model.}, journal = {European urology open science}, volume = {57}, number = {}, pages = {74-83}, doi = {10.1016/j.euros.2023.09.008}, pmid = {38020524}, issn = {2666-1683}, abstract = {BACKGROUND: Next-generation sequencing (NGS) methods for microbial profiling have increased sensitivity to detect urinary pathogens.<br><br>OBJECTIVE: To determine whether NGS microbial profiling can be used to guide antibiotic prophylaxis and reduce infection compared with the standard of care.<br><br>A prospective randomized controlled clinical trial of patients undergoing urologic stone interventions at an academic health center from December 2019 to January 2022 was conducted. Urine was collected at the preoperative visit for standard culture and intervention NGS diagnostics. Evaluable patients were culture negative, met 2-wk follow-up, and did not cancel surgery. Of 240 individuals (control&#xa0;=&#xa0;121, intervention&#xa0;=&#xa0;119), 83 control and 74 intervention patients were evaluable.<br><br>INTERVENTION: Microbial findings (paired quantitative polymerase chain reaction and NGS) were sent to an infectious disease pharmacist to recommend prophylactic antimicrobial regimen.<br><br>The primary outcome was postoperative urinary infection within the follow-up period (Fisher's exact test). The primary outcome was analyzed by modified intent-to-treat (mITT) and per-protocol analyses. Secondary endpoints considered included positive culture concordance, antibiotic use, and adverse events. Additional post hoc analyses investigated factors contributing to infection (univariate logistic regression).<br><br>RESULTS AND LIMITATIONS: The intervention significantly reduced postsurgical urinary infection risk by 7.1% (-0.73%, 15%) compared with the standard of care in the mITT analysis (1.4% vs 8.4%, p&#xa0;=&#xa0;0.045) or by 8.5% (0.88%, 16%) compared with the per-protocol analysis (0% vs 8.5%, p&#xa0;=&#xa0;0.032). NGS-guided treatment altered the distribution of antibiotics used (p&#xa0;=&#xa0;0.025), and antibiotics poorly matched with NGS findings were associated with increased infection odds (odds ratio [OR]&#xa0;=&#xa0;5.9, p&#xa0;=&#xa0;0.046). Women were at greater odds to develop infection (OR&#xa0;=&#xa0;10, p&#xa0;=&#xa0;0.03) and possessed differentiated microbial profiles (p&#xa0;<&#xa0;0.001).<br><br>CONCLUSIONS: Urinary microbial NGS-guided antibiotic prophylaxis before endoscopic urologic stone lithotripsy improves antibiotic selection to reduce healthcare-associated urinary infections; however, treatment efficacy may be limited by the ability to adhere to the recommended protocol.<br><br>PATIENT SUMMARY: We investigated whether microbial DNA sequencing could improve the selection of antibiotics before kidney stone surgery in patients not known to have any bacteria in the urine on standard culture. We found that using microbe DNA to guide antibiotic choices decreased postoperative infection rate and may encourage individualized use of available antibiotics.}, }
@article {pmid38020300, year = {2023}, author = {Liu, W and Li, Z and Li, X and Cao, H and Jiang, H and Niu, Q and Hu, B}, title = {Influence of tumor mycobiome on cancer pathogenesis (Review).}, journal = {Oncology letters}, volume = {26}, number = {6}, pages = {541}, doi = {10.3892/ol.2023.14128}, pmid = {38020300}, issn = {1792-1082}, abstract = {Cancer tissues harbor a large microbiome. There is growing evidence that the tumor microbiome is significantly correlated with the prognosis of cancer patients, but the exact underlying mechanisms have remained elusive. Although the tumor mycobiome is less abundant than the biome of bacteria, it is prevalent in most cancers in humans. The present review describes in detail the impact of the tumor mycobiome on cancer pathogenesis. The tumor mycobiome promotes tumor progression and metastasis by affecting the human immune system, maintaining a pro-inflammatory environment, producing aflatoxins, attenuating cell adhesion mechanisms and fungal-bacterial interactions. Furthermore, the tumor mycobiome likewise has great potential for cancer prevention, diagnosis and treatment.}, }
@article {pmid38020222, year = {2023}, author = {Arakkal Thaiparambil, N and Radhakrishnan, V}, title = {Role of formulated bacterial consortia in biofortifying tomato fruits with nutrients: A nutritional, genomic and metagenomic analysis.}, journal = {Saudi journal of biological sciences}, volume = {30}, number = {12}, pages = {103851}, doi = {10.1016/j.sjbs.2023.103851}, pmid = {38020222}, issn = {1319-562X}, abstract = {Nutrient deficiencies are a major problem that is prone to affect millions of people around the globe. Biofortification, a process of enriching nutrients in staple food crops is an effective method to tackle this malnutrition-associated disorder. Tomato (Solanum lycopersicum) is a globally consumed crop and therefore is a suitable candidate for biofortification. Many plant growth-promoting bacteria are reported to have the ability to enhance nutrient content in plants. In the present study, we have investigated the ability of two bacterial consortia (consortia-1 -co-culturing Lysinibacillus sp. strain VITKC-5 and Acinetobacter Sp. strain VITKC_6; and consortia-2 -co-culturing Lysinibacillus sp. strain VITKC-5 and Enterobacter sp. strain VITVLC-4) in the nutrient enrichment of tomato fruits. The results were then correlated with the elevated expression of nutrient transporter genes. Furthermore, the effect of these bacterial formulations on the indigenous microbiome has also been evaluated through metagenomic analysis. The application of bacterial formulations significantly improved the nutrient content when compared to the control (untreated) group. These findings advocate that PGPB-assisted biofortification has the potential to alleviate nutrient deficiency in humans.}, }
@article {pmid38020091, year = {2023}, author = {Kim, MG and Cho, WY and Chung, SM and Choi, YE and Fang, Y and Park, MS and Park, SJ and Ko, YS and Lee, HY and Yang, J and Oh, SW and Jo, SK}, title = {Altered gut microbiome plays an important role in AKI to CKD transition in aged mice.}, journal = {Frontiers in medicine}, volume = {10}, number = {}, pages = {1238960}, doi = {10.3389/fmed.2023.1238960}, pmid = {38020091}, issn = {2296-858X}, abstract = {INTRODUCTION: This study investigated the role of renal-intestinal crosstalk in the transition from acute kidney injury (AKI) to chronic kidney disease (CKD) in elderly individuals.<br><br>METHODS: Using young and aged mice, we induced bilateral ischemia-reperfusion injury (IRI) and compared intestinal and kidney inflammation over 28&#x2009;days. To determine the role of the microbiome in gut-kidney crosstalk, we analyzed the microbiome of fecal samples of the young vs. aged mice and examined the effects of probiotic supplementation.<br><br>RESULTS: In the post-IRI recovery phase, prolonged intestinal and renal inflammation along with dysbiosis were evident in aged vs. younger mice that was associated with severe renal dysfunction and fibrosis progression in aged mice. Probiotic supplementation with Bifidobacterium bifidum BGN4 and Bifidobacterium longum BORI alleviated intestinal inflammation but not intestinal leakage, characterized by decreased inflammatory cytokine levels and decreased infiltration of macrophages, neutrophils, and Th17 cells. This was associated with improved M1-dominant renal inflammation and ultimately improved renal function and fibrosis, suggesting that renal-intestinal crosstalk in aged mice contributes to the transition from AKI to CKD.<br><br>DISCUSSION: Our study findings suggest that exacerbation of chronic inflammation through the gut-kidney axis might be an important mechanism in the transition from AKI to CKD in the elderly.}, }
@article {pmid38019934, year = {2023}, author = {Agarwal, K and Choudhury, B and Robinson, LS and Morrill, SR and Bouchibiti, Y and Chilin-Fuentes, D and Rosenthal, SB and Fisch, KM and Peipert, JF and Lebrilla, CB and Allsworth, JE and Lewis, AL and Lewis, WG}, title = {Resident microbes shape the vaginal epithelial glycan landscape.}, journal = {Science translational medicine}, volume = {15}, number = {724}, pages = {eabp9599}, doi = {10.1126/scitranslmed.abp9599}, pmid = {38019934}, issn = {1946-6242}, abstract = {Epithelial cells are covered in carbohydrates (glycans). This glycan coat or "glycocalyx" interfaces directly with microbes, providing a protective barrier against potential pathogens. Bacterial vaginosis (BV) is a condition associated with adverse health outcomes in which bacteria reside in direct proximity to the vaginal epithelium. Some of these bacteria, including Gardnerella, produce glycosyl hydrolase enzymes. However, glycans of the human vaginal epithelial surface have not been studied in detail. Here, we elucidate key characteristics of the "normal" vaginal epithelial glycan landscape and analyze the impact of resident microbes on the surface glycocalyx. In human BV, glycocalyx staining was visibly diminished in electron micrographs compared to controls. Biochemical and mass spectrometric analysis showed that, compared to normal vaginal epithelial cells, BV cells were depleted of sialylated N- and O-glycans, with underlying galactose residues exposed on the surface. Treatment of primary epithelial cells from BV-negative women with recombinant Gardnerella sialidases generated BV-like glycan phenotypes. Exposure of cultured VK2 vaginal epithelial cells to recombinant Gardnerella sialidase led to desialylation of glycans and induction of pathways regulating cell death, differentiation, and inflammatory responses. These data provide evidence that vaginal epithelial cells exhibit an altered glycan landscape in BV and suggest that BV-associated glycosidic enzymes may lead to changes in epithelial gene transcription that promote cell turnover and regulate responses toward the resident microbiome.}, }
@article {pmid38019873, year = {2023}, author = {Bar, O and Sudhof, LS and Yockey, LJ and Bergerat, A and Moriel, N and Andrews, E and Ananthakrishnan, AN and Xavier, RJ and Yassour, M and Mitchell, CM}, title = {Comparison of vaginal microbiota between women with inflammatory bowel disease and healthy controls.}, journal = {PloS one}, volume = {18}, number = {11}, pages = {e0284709}, doi = {10.1371/journal.pone.0284709}, pmid = {38019873}, issn = {1932-6203}, abstract = {BACKGROUND: The gut microbiota in patients with inflammatory bowel disease are perturbed in both composition and function. The vaginal microbiome and its role in the reproductive health of women with inflammatory bowel disease is less well described.<br><br>OBJECTIVE: We aim to compare the vaginal microbiota of women with inflammatory bowel disease to healthy controls.<br><br>METHODS: Women with inflammatory bowel disease enrolled in a longitudinal cohort study provided self-collected vaginal swabs. Healthy controls underwent provider-collected vaginal swabs at routine gynecologic exams. All participants completed surveys on health history, vulvovaginal symptoms and gastrointestinal symptoms, if applicable. Microbiota were characterized by sequencing the V4 region of the 16S rRNA gene. Associations between patient characteristics and microbial community composition were evaluated by PERMANOVA and Principal Components Analysis. Lactobacillus dominance of the microbial community was compared between groups using chi-square and Poisson regression.<br><br>RESULTS: The cohort included 54 women with inflammatory bowel disease (25 Ulcerative colitis, 25 Crohn's Disease) and 26 controls. A majority, 72 (90%) were White; 17 (31%) with inflammatory bowel disease and 7 (27%) controls were postmenopausal. The composition of the vaginal microbiota did not vary significantly by diagnosis or severity of inflammatory bowel disease but did vary by menopausal status (p = 0.042). There were no significant differences in Shannon Diversity Index between healthy controls and women with IBD in premenopausal participants. There was no difference in proportion of Lactobacillus dominance according to diagnosis in premenopausal participants. A subgroup of postmenopausal women with Ulcerative colitis showed a significant higher alpha diversity and a lack of Lactobacillus dominance in the vaginal microbiome.<br><br>CONCLUSIONS: Menopausal status had a larger impact on vaginal microbial communities than inflammatory bowel disease diagnosis or severity.}, }
@article {pmid38019089, year = {2023}, author = {Muñoz, E and Fuentes, F and Felmer, R and Arias, ME and Yeste, M}, title = {Effects of reactive oxygen and nitrogen species stress on male fertility.}, journal = {Antioxidants &amp; redox signaling}, volume = {}, number = {}, pages = {}, doi = {10.1089/ars.2022.0163}, pmid = {38019089}, issn = {1557-7716}, abstract = {SIGNIFICANCE: In recent decades, male fertility has been severely reduced worldwide. The causes underlying this decline are multifactorial and include, among others, genetic alterations, changes in the microbiome, and the impact of environmental pollutants. Such factors have in common that they can dysregulate physiological levels of reactive species of oxygen (ROS) and nitrogen (RNS) in the patient, generating oxidative and nitrosative stress that impairs fertility.<br><br>RECENT ADVANCES: Recent studies have delved into other factors involved in the dysregulation of ROS and RNS levels, such as diet, obesity, persistent infections, environmental pollutants and gut microbiota, thus leading to new strategies to solve male fertility problems, such as consuming prebiotics to regulate gut flora or treating psychological conditions.<br><br>CRITICAL ISSUES: The pathways where ROS or RNS may be involved as modulators are still under investigation. Moreover, the extent to which treatments can rescue male infertility as well as whether they may have side effects remain, in most cases, to be elucidated. For example, it is known that prescription of antioxidants to treat nitrosative stress can alter sperm chromatin condensation, which makes DNA more exposed to ROS and RNS, and may thus affect fertilization and early embryo development.<br><br>FUTURE DIRECTIONS: The involvement of extracellular vesicles, which might play a crucial role in cell communication during spermatogenesis and epididymal maturation, and the relevance of other factors like sperm epigenetic signatures should be envisaged in the future.}, }
@article {pmid38018983, year = {2023}, author = {Panyod, S and Wu, W-K and Hu, M-Y and Huang, H-S and Chen, R-A and Chen, Y-H and Shen, T-CD and Ho, C-T and Liu, C-J and Chuang, H-L and Huang, C-C and Wu, M-S and Sheen, L-Y}, title = {Healthy diet intervention reverses the progression of NASH through gut microbiota modulation.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0186823}, doi = {10.1128/spectrum.01868-23}, pmid = {38018983}, issn = {2165-0497}, abstract = {The link between gut microbiota and diet is crucial in the development of non-alcoholic steatohepatitis (NASH). This study underscores the essential role of a healthy diet in preventing and treating NASH by reversing obesity, lipidemia, and gut microbiota dysbiosis. Moreover, the supplementation of functional food or drug to the diet can provide additional advantages by inhibiting hepatic inflammation through the modulation of the hepatic inflammasome signaling pathway and partially mediating the gut microbiota and lipopolysaccharide signaling pathway. This study highlights the importance of adopting healthy dietary habits in treating NASH and proposes that supplementing with ginger essential oil or obeticholic acid may offer additional benefits. Nonetheless, further clinical studies are necessary to validate these findings.}, }
@article {pmid38018965, year = {2023}, author = {Ottesen, A and Kocurek, B and Deaver, C and Chiesa, O and Cohen, R and Reed, E and Commichaux, S and Mammel, M and McDermott, P and Strain, E and Myers, M}, title = {Fecal microbiomes of laboratory beagles receiving antiparasitic formulations in an experimental setting.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0086023}, doi = {10.1128/MRA.00860-23}, pmid = {38018965}, issn = {2576-098X}, abstract = {Here, we describe the fecal microbiome of laboratory beagles in a non-invasive experiment designed to contrast in vivo versus in vitro bioequivalence in response to antiparasitic drug administration. The experiment provided a unique opportunity to evaluate metagenomic profiles of canine feces before and after anti-parasitic drug exposure.}, }
@article {pmid38018964, year = {2023}, author = {Nguyen, VH and Sharon, BM and Shipman, BM and Zimmern, PE and De Nisco, NJ}, title = {Complete genomes of Limosilactobacillus portuensis and Limosilactobacillus vaginalis isolated from the urine of postmenopausal women.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0088323}, doi = {10.1128/MRA.00883-23}, pmid = {38018964}, issn = {2576-098X}, abstract = {There is frequent evidence that Limosilactobacillus vaginalis colonizes female genitourinary tracts but few reports of Limosilactobacillus portuensis. Their role in urinary tract infection (UTI) is unclear. We present the first complete genome of L. portuensis and a complete genome of L. vaginalis isolated from postmenopausal women with varying UTI histories.}, }
@article {pmid38018859, year = {2023}, author = {Ramamoorthy, S and Pena, M and Ghosh, P and Liao, Y-Y and Paret, M and Jones, JB and Potnis, N}, title = {Transcriptome profiling of type VI secretion system core gene tssM mutant of Xanthomonas perforans highlights regulators controlling diverse functions ranging from virulence to metabolism.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0285223}, doi = {10.1128/spectrum.02852-23}, pmid = {38018859}, issn = {2165-0497}, abstract = {T6SS has received attention due to its significance in mediating interorganismal competition through contact-dependent release of effector molecules into prokaryotic and eukaryotic cells. Reverse-genetic studies have indicated the role of T6SS in virulence in a variety of plant pathogenic bacteria, including the one studied here, Xanthomonas. However, it is not clear whether such effect on virulence is merely due to a shift in the microbiome-mediated protection or if T6SS is involved in a complex virulence regulatory network. In this study, we conducted in vitro transcriptome profiling in minimal medium to decipher the signaling pathways regulated by tssM-i3* in X. perforans AL65. We show that TssM-i3* regulates the expression of a suite of genes associated with virulence and metabolism either directly or indirectly by altering the transcription of several regulators. These findings further expand our knowledge on the intricate molecular circuits regulated by T6SS in phytopathogenic bacteria.}, }
@article {pmid38018836, year = {2023}, author = {Bishu, S and Ginnebaugh, B and Chu, J and Levy, BH and , }, title = {Microbiome-Based Therapeutics in Digestive Diseases: What They Are and How Are They Regulated.}, journal = {Clinical and translational gastroenterology}, volume = {14}, number = {11}, pages = {e00636}, doi = {10.14309/ctg.0000000000000636}, pmid = {38018836}, issn = {2155-384X}, }
@article {pmid38018203, year = {2023}, author = {Meda, A and Fredrick, F and Rathod, U and Shah, P and Jain, R}, title = {Cardiovascular Manifestations in Inflammatory Bowel Disease.}, journal = {Current cardiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.2174/011573403X256094231031074753}, pmid = {38018203}, issn = {1875-6557}, abstract = {Inflammatory bowel disease is a group of long-term systemic inflammatory disorders affecting the gastrointestinal tract, including Crohn's disease and ulcerative colitis, which may be associated with an increased risk of developing extraintestinal manifestations, including cardiovascular disease, thereby decreasing the quality of life. Pathophysiological changes associated with inflammatory bowel disease include alterations of the microbiome, endotoxemia, and changes to glucose and lipid metabolism. Inflammatory bowel disease patients have higher carotid intima-media thickness, lower flow-mediated dilatation, and increased carotid-femoral pulse wave velocity, which are markers of elevated cardiovascular risk. In addition, inflammatory bowel disease patients are at an increased risk for developing venous and arterial thrombotic events due to a hypercoagulable state caused by thrombocytosis and coagulation system activation. To reduce the risk of developing cardiovascular disease, lifestyle modifications, such as smoking cessation, dietary changes, and increased physical activity alongside management with appropriate medication, should be considered. This research paper examines how inflammatory bowel disease can influence the risk of cardiovascular complications and the involvement of drug therapy. Methods: PubMed was searched using keywords, such as inflammatory bowel disease, Crohn's disease, ulcerative colitis, cardiovascular disease, pericarditis, thromboembolism, and many more. Relevant literature up to March 2023 has been examined and summarized, which consisted of data from various clinical trials, meta-analyses, retrospective/prospective cohort studies, and current guidelines.}, }
@article {pmid38018189, year = {2023}, author = {Zheng, Y and Liu, J and Beeraka, NM and Manogaran, P and Vikram P R, H and Yn, LD and Suhail, SM and Pradeepkumar, B and Sinelnikov, MY and Greeshma, MV and P A, M and Mp, N and Bannimath, G and Zhao, J and Fan, R}, title = {Inflammation and Stem Cell Stochasticity of HPV-induced Cervical Cancer: Epigenetics Based Biomarkers through Microbiome and Metabolome for Personalized Medicine: A Systematic Review.}, journal = {Current medicinal chemistry}, volume = {}, number = {}, pages = {}, doi = {10.2174/0109298673257429231108072717}, pmid = {38018189}, issn = {1875-533X}, abstract = {BACKGROUND: Chemoresistance by stemness in HPV-induced cervical carcinogenesis has significant implications for the overall disease-specific survival of the patients. To date, there are no reports related to the implications of significant aspects of inflammation and microbiome-- mediated epigenetics in cervical cancers.<br><br>OBJECTIVE: The current systematic review delineates the significant aspects of the inflammation-related pathophysiology, cervical cancer diagnosis based on the HPV-indued stemness, and microbiome- mediated epigenetic markers to develop personalized therapies to target the stemness-acquired indefinitely dividing cancer stem cells.<br><br>METHODS: We performed a systematic review without a meta- analysis. We searched several public databases, such as Pubmed, ReleMed, National Library of Medicine, and Scopus, related to inflammation, metabolomics, microbiome-mediated epigenetic markers, and HPV-induced stemness.<br><br>RESULTS AND CONCLUSION: The review significantly described the correlation between microbial inflammation and stem cell stochasticity of HPV-Induced cervical cancer and the expression of epigenetics- based biomarkers through microbiome and metabolome to foster the cervical cancer progression. These are major risk factors that can cause cervical dysplasia with substantial therapy resistance in cervical cancer patients. The qualitative and quantitative examination of the spatial transcriptomic expression of these stemness markers in the dividing cervical cancer stem cells has significant implications in the clinical sector to develop early personalized medicine to prevent cervical precancerous lesions depending on the prognosis of the cervical cancer patients. Mainly, the combinatorial regimen of current therapeutic modalities, along with microbiome-related therapies with future landscape of epigenetics-modulated therapies, may enhance overall disease-specific survival by modulating the stochastic dynamics of basal epithelial cells across the cervical region.}, }
@article {pmid38018103, year = {2023}, author = {Xu, CCY and Lemoine, J and Albert, A and Whirter, &#xc9;M and Barrett, RDH}, title = {Community assembly of the human piercing microbiome.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {2011}, pages = {20231174}, doi = {10.1098/rspb.2023.1174}, pmid = {38018103}, issn = {1471-2954}, abstract = {Predicting how biological communities respond to disturbance requires understanding the forces that govern their assembly. We propose using human skin piercings as a model system for studying community assembly after rapid environmental change. Local skin sterilization provides a 'clean slate' within the novel ecological niche created by the piercing. Stochastic assembly processes can dominate skin microbiomes due to the influence of environmental exposure on local dispersal, but deterministic processes might play a greater role within occluded skin piercings if piercing habitats impose strong selection pressures on colonizing species. Here we explore the human ear-piercing microbiome and demonstrate that community assembly is predominantly stochastic but becomes significantly more deterministic with time, producing increasingly diverse and ecologically complex communities. We also observed changes in two dominant and medically relevant antagonists (Cutibacterium acnes and Staphylococcus epidermidis), consistent with competitive exclusion induced by a transition from sebaceous to moist environments. By exploiting this common yet uniquely human practice, we show that skin piercings are not just culturally significant but also represent ecosystem engineering on the human body. The novel habitats and communities that skin piercings produce may provide general insights into biological responses to environmental disturbances with implications for both ecosystem and human health.}, }
@article {pmid38018034, year = {2023}, author = {Chen, Y and Lu, Y and Wang, T and Wu, J and Yu, B}, title = {Changes in Gut Microbiota at 1-60 Days in 92 Preterm Infants in a Neonatal Intensive Care Unit Using 16S rRNA Gene Sequencing.}, journal = {Medical science monitor : international medical journal of experimental and clinical research}, volume = {29}, number = {}, pages = {e941560}, doi = {10.12659/MSM.941560}, pmid = {38018034}, issn = {1643-3750}, abstract = {BACKGROUND Neonatal gut diversity is influenced by birth conditions and probiotic/antibiotic use. The gut microbiota affects brain development, immunity, and risk of diseases. Preterm infants, especially in neonatal intensive care units (NICUs), have different gut flora from full-term infants, suggesting in utero microbial colonization. This study examined gut microbiota changes in 92 NICU preterm infants in China. MATERIAL AND METHODS We collected data on 92 preterm infants admitted to the NICU immediately after birth, and fecal samples were collected on days 1, 3, 7, 14, 21, 28, and 60. We analyzed changes in intestinal bacteria through 16S rRNA sequencing, predicted the change in gut microbiota function over time, and compared the effects of main feeding modality on the intestinal bacteria of preterm infants. RESULTS At the phylum level, the top 5 phyla in total accounted for 99.69% of the abundance, in decreasing order of abundance: Proteobacteria, Firmicutes, Actinobacteria, Tenericutes, and Bacteroidetes. At the genus level, the top 10 genera in terms of abundance accounted for a total of 90.90%, in decreasing order of abundance: Pseudomonas, Staphylococcus, Klebsiella, Escherichia-Shigella, unclassified Enterobacteriaceae, Staphylococcus, Clostridium-sensu-stricto-1, Streptococcus, Sphingomonas, and Ureaplasma. The abundance of Proteobacteria and Pseudomonas showed a decreasing trend at first, reached a minimum at day 14, and then an increasing trend, while the opposite trend was observed for Firmicutes. The metabolic function of the bacterial community changed greatly at different time points. The abundance of Proteobacteria at the phylum level and Streptococcus at the genus level in formula-fed infants were significantly higher than in breast-fed infants. CONCLUSIONS Between 1 and 60 days, the gut microbiome in preterm infants in the NICU changed with changes in feeding patterns, with the main gut bacteria being from the phyla, Proteobacteria, and Pseudomonas.}, }
@article {pmid38017662, year = {2023}, author = {Brushett, S and Gacesa, R and Vich Vila, A and Brandao Gois, MF and Andreu-Sánchez, S and Swarte, JC and Klaassen, MAY and Collij, V and Sinha, T and Bolte, LA and Wu, J and Swertz, M and de Kroon, MLA and Reijneveld, SA and Wijmenga, C and Weersma, RK and Fu, J and van Loo, HM and Kurilshikov, A and Zhernakova, A}, title = {Gut feelings: the relations between depression, anxiety, psychotropic drugs and the gut microbiome.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2281360}, doi = {10.1080/19490976.2023.2281360}, pmid = {38017662}, issn = {1949-0984}, abstract = {The gut microbiome is involved in the bi-directional relationship of the gut - brain axis. As most studies of this relationship are small and do not account for use of psychotropic drugs (PTDs), we explored the relations of the gut microbiome with several internalizing disorders, while adjusting for PTDs and other relevant medications, in 7,656 Lifelines participants from the Northern Netherlands (5,522 controls and 491 participants with at least one internalizing disorder). Disorders included dysthymia, major depressive disorder (MDD), any depressive disorder (AnyDep: dysthymia or MDD), generalized anxiety disorder (GAD) and any anxiety disorder (AnyAnx: GAD, social phobia and panic disorder). Compared to controls, 17 species were associated with depressive disorders and 3 were associated with anxiety disorders. Around 90% of these associations remained significant (FDR <0.05) after adjustment for PTD use, suggesting that the disorders, not PTD use, drove these associations. Negative associations were observed for the butyrate-producing bacteria Ruminococcus bromii in participants with AnyDep and for Bifidobacterium bifidum in AnyAnx participants, along with many others. Tryptophan and glutamate synthesis modules and the 3,4-Dihydroxyphenylacetic acid synthesis module (related to dopamine metabolism) were negatively associated with MDD and/or dysthymia. After additional adjustment for functional gastrointestinal disorders and irritable bowel syndrome, these relations remained either statistically (FDR <0.05) or nominally (P < 0.05) significant. Overall, multiple bacterial species and functional modules were associated with internalizing disorders, including gut - brain relevant components, while associations to PTD use were moderate. These findings suggest that internalizing disorders rather than PTDs are associated with gut microbiome differences relative to controls.}, }
@article {pmid38017581, year = {2023}, author = {Lin, D and Hong, J and Sanogo, B and Du, S and Xiang, S and Hui, JH and Ding, T and Wu, Z and Sun, X}, title = {Core gut microbes Cloacibacterium and Aeromonas associated with different gastropod species could be persistently transmitted across multiple generations.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {267}, pmid = {38017581}, issn = {2049-2618}, support = {82202560, 82161160343 and 82272361//the National Natural Science Foundation of China/ ; 82202560, 82161160343 and 82272361//the National Natural Science Foundation of China/ ; 82202560, 82161160343 and 82272361//the National Natural Science Foundation of China/ ; 22qntd4813//the Fundamental Research Funds for the Central Universities/ ; NPRC-2019-194-30//the National Parasitic Resource Center of China and the Ministry of Science and Technology/ ; N_CUHK401/21//the NSFC/RGC Joint Research Scheme/ ; 2022B1111030002//the R&amp;D Program in Key Areas of Guangdong Province/ ; 20201192//the 6th Nuclear Energy R&amp;D Project/ ; B12003//the 111 Project/ ; 2020YFC1200100, 2020YFC1200103, 2021YFC2300800 and 2016YFC1200500//the National Key R&amp;D Program of China/ ; 2021B1212040017//the Science and Technology Planning Project of Guangdong Province/ ; }, abstract = {BACKGROUND: Studies on the gut microbiota of animals have largely focused on vertebrates. The transmission modes of commensal intestinal bacteria in mammals have been well studied. However, in gastropods, the relationship between gut microbiota and hosts is still poorly understood. To gain a better understanding of the composition of gut microbes and their transmission routes in gastropods, a large-scale and long-term experiment on the dynamics and transmission modes of gut microbiota was conducted on freshwater snails.<br><br>RESULTS: We analyzed 244 microbial samples from the digestive tracts of freshwater gastropods and identified Proteobacteria and Bacteroidetes as dominant gut microbes. Aeromonas, Cloacibacterium, and Cetobacterium were identified as core microbes in the guts, accounting for over 50% of the total sequences. Furthermore, both core bacteria Aeromonas and Cloacibacterium, were shared among 7 gastropod species and played an important role in determining the gut microbial community types of both wild and cultured gastropods. Analysis of the gut microbiota at the population level, including wild gastropods and their offspring, indicated that a proportion of gut microbes could be consistently vertically transmitted inheritance, while the majority of the gut microbes resulted from horizontal transmission. Comparing cultured snails to their wild counterparts, we observed an increasing trend in the proportion of shared microbes and a decreasing trend in the number of unique microbes among wild gastropods and their offspring reared in a cultured environment. Core gut microbes, Aeromonas and Cloacibacterium, remained persistent and dispersed from wild snails to their offspring across multiple generations. Interestingly, under cultured environments, the gut microbiota in wild gastropods could only be maintained for up to 2 generations before converging with that of cultured snails. The difference observed in gut bacterial metabolism functions was associated with this transition. Our study also demonstrated that the gut microbial compositions in gastropods are influenced by developmental stages and revealed the presence of Aeromonas and Cloacibacterium throughout the life cycle in gastropods. Based on the dynamics of core gut microbes, it may be possible to predict the health status of gastropods during their adaptation to new environments. Additionally, gut microbial metabolic functions were found to be associated with the adaptive evolution of gastropods from wild to cultured environments.<br><br>CONCLUSIONS: Our findings provide novel insights into the dynamic processes of gut microbiota colonization in gastropod mollusks and unveil the modes of microbial transmission within their guts. Video Abstract.}, }
@article {pmid38017526, year = {2023}, author = {Poulsen, JS and Macêdo, WV and Bonde, T and Nielsen, JL}, title = {Energetically exploiting lignocellulose-rich residues in anaerobic digestion technologies: from bioreactors to proteogenomics.}, journal = {Biotechnology for biofuels and bioproducts}, volume = {16}, number = {1}, pages = {183}, pmid = {38017526}, issn = {2731-3654}, support = {NNF16OC0021818//Novo Nordisk Fonden/ ; NNF16OC0021818//Novo Nordisk Fonden/ ; }, abstract = {The biogas produced through anaerobic digestion (AD) of renewable feedstocks is one of the promising alternatives to replace fossil-derived energy. Even though lignocellulosic biomass is the most abundant biomass on earth, only a small fraction is being used towards resources recovery, leaving a great potential unexploited. In this study, the combination of state-of-art genomic techniques and engineered systems were used to further advance the knowledge on biogas production from lignocellulosic-rich residues and the microbiome involved in the anaerobic digestion hereof. A long-term adapted anaerobic microbiome capable of degrading wheat straw as the sole substrate was investigated using protein stable isotope probing (protein-SIP). The results indicated that a diverse microbial community, primarily composed of Firmicutes and Methanogens, played crucial roles in cellulose degradation and methane production. Notably, Defluviitoga tunisiensis, Syntrophothermus lipocalidus, and Pelobacter carbinolicus were identified as direct metabolizers of cellulose, while Dehalobacterium assimilated labelled carbon through cross-feeding. This study provides direct evidence of primary cellulose degraders and sheds light on their genomic composition. By harnessing the potential of lignocellulosic biomass and understanding the microbial communities involved, we can promote sustainable biogas production, contributing to energy security and environmental preservation.}, }
@article {pmid38017525, year = {2023}, author = {Bakker, JW and Begemann, HLM and Fonville, M and Esser, HJ and de Boer, WF and Sprong, H and Koenraadt, CJM}, title = {Differential associations of horizontally and vertically transmitted symbionts on Ixodes ricinus behaviour and physiology.}, journal = {Parasites &amp; vectors}, volume = {16}, number = {1}, pages = {443}, pmid = {38017525}, issn = {1756-3305}, abstract = {BACKGROUND: Ixodes ricinus ticks are infected with a large diversity of vertically and horizontally transmitted symbionts. While horizontally transmitted symbionts rely on a vertebrate host for their transmission, vertically transmitted symbionts rely more on the survival of their invertebrate host for transmission. We therefore hypothesized horizontally transmitted symbionts to be associated with increased tick activity to increase host contact rate and vertically transmitted symbionts to be associated with higher tick weight and lipid fraction to promote tick survival.<br><br>METHODS: We used a behavioural assay to record the questing activity of I. ricinus ticks. In addition, we measured weight and lipid fraction and determined the presence of ten symbiont species in these ticks using qPCR, of which six were vertically transmitted and four horizontally transmitted.<br><br>RESULTS: Vertically transmitted symbionts (e.g. Midichloria mitochondrii) were associated with an increase in tick weight, whereas horizontally transmitted symbionts (e.g. Borrelia burgdorferi sensu lato) were often associated with lower weight and lipid fraction of ticks. Moreover, horizontally transmitted symbionts (e.g. B. burgdorferi s.l.) were associated with increased tick activity, which may benefit pathogen transmission and increases tick-borne disease hazard.<br><br>CONCLUSIONS: Our study shows that horizontally and vertically transmitted symbionts differentially influence the behaviour and physiology of I. ricinus and warrants future research to study the underlying mechanisms and effects on transmission dynamics of tick-borne pathogens.}, }
@article {pmid38017392, year = {2023}, author = {Jensen, MG and Svraka, L and Baez, E and Lund, M and Poehlein, A and Brüggemann, H}, title = {Species- and strain-level diversity of Corynebacteria isolated from human facial skin.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {366}, pmid = {38017392}, issn = {1471-2180}, support = {LF-OC-21-000826//LEO Fondet/ ; }, abstract = {BACKGROUND: Sequencing of the human skin microbiome revealed that Corynebacterium is an ubiquitous and abundant bacterial genus on human skin. Shotgun sequencing further highlighted the microbial "dark matter" of the skin microbiome, consisting of microorganisms, including corynebacterial species that were not cultivated and genome-sequenced so far. In this pilot project, facial human skin swabs of 13 persons were cultivated to selectively obtain corynebacteria. 54 isolates were collected and 15 of these were genome-sequenced and the pan-genome was determined. The strains were biochemically characterized and antibiotic susceptibility testing (AST) was performed.<br><br>RESULTS: Among the 15 sequenced strains, nine different corynebacterial species were found, including two so far undescribed species, tentatively named "Corynebacterium vikingii" and "Corynebacterium borealis", for which closed genome sequences were obtained. Strain variability beyond the species level was determined in biochemical tests, such as the variable presence of urease activity and the capacity to ferment different sugars. The ability to grow under anaerobic conditions on solid agar was found to be species-specific. AST revealed resistances to clindamycin in seven strains. A Corynebacterium pseudokroppenstedtii strain showed additional resistance towards beta-lactam and fluoroquinolone antibiotics; a chromosomally located 17&#xa0;kb gene cluster with five antibiotic resistance genes was found in the closed genome of this strain.<br><br>CONCLUSIONS: Taken together, this pilot study identified an astonishing diversity of cutaneous corynebacterial species in a relatively small cohort and determined species- and strain-specific individualities regarding biochemical and resistance profiles. This further emphasizes the need for cultivation-based studies to be able to study these microorganisms in more detail, in particular regarding their host-interacting and, potentially, -beneficial and/or -detrimental properties.}, }
@article {pmid38017389, year = {2023}, author = {Tsakmaklis, A and Farowski, F and Zenner, R and Lesker, TR and Strowig, T and Schlößer, H and Lehmann, J and von Bergwelt-Baildon, M and Mauch, C and Schlaak, M and Knuever, J and Schweinsberg, V and Heinzerling, LM and Vehreschild, MJGT}, title = {TIGIT[+] NK cells in combination with specific gut microbiota features predict response to checkpoint inhibitor therapy in melanoma patients.}, journal = {BMC cancer}, volume = {23}, number = {1}, pages = {1160}, pmid = {38017389}, issn = {1471-2407}, support = {70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; }, abstract = {BACKGROUND: Composition of the intestinal microbiota has been correlated to therapeutic efficacy of immune checkpoint inhibitors (ICI) in various cancer entities including melanoma. Prediction of the outcome of such therapy, however, is still unavailable. This prospective, non-interventional study was conducted in order to achieve an integrated assessment of the connection between a specific intestinal microbiota profile and antitumor immune response to immune checkpoint inhibitor therapy (anti-PD-1 and/or anti-CTLA-4) in melanoma patients.<br><br>METHODS: We assessed blood and stool samples of 29 cutaneous melanoma patients who received immune checkpoint inhibitor therapy. For functional and phenotypical immune analysis, 12-color flow cytometry and FluoroSpot assays were conducted. Gut microbiome was analyzed with shotgun metagenomics sequencing. To combine clinical, microbiome and immune variables, we applied the Random Forest algorithm.<br><br>RESULTS: A total of 29 patients was analyzed in this study, among whom 51.7% (n&#x2009;=&#x2009;15) reached a durable clinical benefit. The Immune receptor TIGIT is significantly upregulated in T cells (p&#x2009;=&#x2009;0.0139) and CD56[high] NK cells (p&#x2009;=&#x2009;0.0037) of responders. Several bacterial taxa were associated with response (e.g. Ruminococcus torques) or failure (e.g. Barnesiella intestinihominis) to immune therapy. A combination of two microbiome features (Barnesiella intestinihominis and the Enterobacteriaceae family) and one immune feature (TIGIT[+] CD56[high] NK cells) was able to predict response to ICI already at baseline (AUC&#x2009;=&#x2009;0.85; 95% CI: 0.841-0.853).<br><br>CONCLUSIONS: Our results reconfirm a link between intestinal microbiota and response to ICI therapy in melanoma patients and furthermore point to TIGIT as a promising target for future immunotherapies.}, }
@article {pmid38016991, year = {2023}, author = {Auger, L and Bouslama, S and Deschamps, MH and Vandenberg, G and Derome, N}, title = {Author Correction: Absence of microbiome triggers extensive changes in the transcriptional profile of Hermetia illucens during larval ontogeny.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {20959}, doi = {10.1038/s41598-023-48023-6}, pmid = {38016991}, issn = {2045-2322}, }
@article {pmid38016587, year = {2023}, author = {Yuan, X and Wu, D and Zhang, D and He, C and Wang, Z and Xu, W and Shou, N and Fu, K and Yue, M and Zhang, X and Shi, Z}, title = {Combining microbiome and pseudotargeted metabolomics revealed the alleviative mechanism of Cupriavidus sp. WS2 on the cadmium toxicity in Vicia unijuga A.Br.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {123040}, doi = {10.1016/j.envpol.2023.123040}, pmid = {38016587}, issn = {1873-6424}, abstract = {Cadmium (Cd) pollution is one of the most severe toxic metals pollution in grassland. Vicia unijuga (V. unijuga) A.Br. planted nearby the grassland farming are facing the risk of high Cd contamination. Here, we investigated the beneficial effects of a highly Cd tolerant rhizosphere bacterium, Cupriavidus sp. WS2, on Cd contaminated V. unijuga. Through plot experiments, we set up four groups of treatments: the control group (without WS2 or Cd), the Cd group (with only Cd addition), the WS2 group (with only WS2 addition), and the WS2/Cd group (with WS2 and Cd addition), and analyzed the changes in physiological indicators, rhizosphere microorganisms, and stem and leaf metabolites of V. unijuga. Results of physiological indicators indicated that Cupriavidus sp. WS2 had strong absorption and accumulation capacity of Cd, exogenous addition of strain WS2 remarkably decreased the Cd concentrations, and increased the plant heights, the biomass, the total protein concentrations, the chlorophyll contents and the photosynthetic rate in stems and leaves of V. unijuga under Cd stress. Cd treatment increased the abundance of Cd tolerant bacterial genera in rhizosphere microbiome, but these genera were down-regulated in the WS2/Cd group. Pseudotargeted metabolomic results showed that six common differential metabolites associated with antioxidant stress were increased after co-culture with WS2. In addition, WS2 activated the antioxidant system including glutathione (GSH) and catalase (CAT), reduced the contents of oxidative stress markers including malondialdehyde (MDA) and hydrogen peroxide (H2O2) in V. unijuga under Cd stress. Taken together, this study revealed that Cupriavidus sp.WS2 alleviated the toxicity of V. unijuga under Cd exposure by activating the antioxidant system, increasing the antioxidant metabolites, and reducing the oxidative stress markers.}, }
@article {pmid38016577, year = {2023}, author = {He, X and Zhou, HX and Fu, X and Ni, KD and Lin, AZ and Zhang, LT and Yin, HH and Jiang, Q and Zhou, X and Meng, YW and Liu, JY}, title = {Metabolomics study reveals increased deoxycholic acid contributes to deoxynivalenol-mediated intestinal barrier injury.}, journal = {Life sciences}, volume = {336}, number = {}, pages = {122302}, doi = {10.1016/j.lfs.2023.122302}, pmid = {38016577}, issn = {1879-0631}, abstract = {AIMS: Deoxynivalenol (DON), namely vomitoxin, is one of the most prevalent fungal toxins in cereal crops worldwide. However, the underlying toxic mechanisms of DON remain largely unknown.<br><br>MAIN METHODS: DON exposure-caused changes in the murine plasma metabolome and gut microbiome were investigated by an LC-MS/MS-based nontargeted metabolomics approach and sequencing of 16S rRNA in fecal samples, respectively. Cellular models were then used to validate the findings from the metabolomics study.<br><br>KEY FINDINGS: DON exposure increased intestinal barrier permeability evidenced by its-mediated decrease in colonic Claudin 5 and E-cadherin, as well as increases in colonic Ifn-&#x3b3;, Cxcl9, Cxcl10, and Cxcr3. Furthermore, DON exposure resulted in a significant increase in murine plasma levels of deoxycholic acid (DCA). Also, DON exposure led to gut microbiota dysbiosis, which was associated with DON exposure-caused increase in plasma DCA. In addition, we found not only DON but also DCA dose-dependently caused a significant increase in the levels of IFN-&#x3b3;, CXCL9, CXCL10, and/or CXCR3, as well as a significant decrease in the expression levels of Claudin 5 and/or E-cadherin in the human colonic epithelial cells (NCM460).<br><br>SIGNIFICANCE: DON-mediated increase in DCA contributes to DON-caused intestinal injury. DCA may be a potential therapeutic target for DON enterotoxicity.}, }
@article {pmid38016505, year = {2023}, author = {Li, S and Chen, T and Zhou, Y and Li, X}, title = {Palmitic acid and trans-4-hydroxy-3-methoxycinnamate, the active ingredients of Yaobishu formula, reduce inflammation and pain by regulating gut microbiota and metabolic changes after lumbar disc herniation to activate autophagy and the Wnt/β-catenin pathway.}, journal = {Biochimica et biophysica acta. Molecular basis of disease}, volume = {}, number = {}, pages = {166972}, doi = {10.1016/j.bbadis.2023.166972}, pmid = {38016505}, issn = {1879-260X}, abstract = {The imbalance in gut microbiota triggers an inflammatory response that spreads from the gut to the discs and is associated with lumbar disc herniation (LDH). In this study, we investigated the mechanism of palmitic acid (PA) and trans-4-hydroxy-3-methoxycinnamic acid (THMC) on microbiota, metabolic homeostasis, and autophagy after LDH. The LDH rat model was established by puncturing the exposed intervertebral disc. 16S rDNA was used to assess the gut microbiome composition. The microbial metabolites were analyzed by UPLC-MS. The mechanism of PA and THMC in LDH was explored by fecal microbiota transplantation (FMT). We found that Yaobishu, PA, THMC, and the positive control drug Celebrex attenuated intervertebral disc damage in LDH rats and downregulated TRPV1, IL-1β, and IL-18 expression. In addition, Yaobishu reduced Oscillospirales and Ruminococcaceae abundances after LDH. PA increased Bacilli's abundance while decreasing Negativicutes and Ruminococcaceae abundances. Metabolomics showed that Yaobishu increased 2-hexanone, methyl isobutyl ketone, 2-methylpentan-3-one, and nonadecanoic acid levels but decreased pantetheine and urocanate levels. PA and THMC reduced uridine and urocanate levels. Yaobishu, PA, and THMC activated autophagy and the Wnt/β-catenin pathway in LDH rats. Moreover, antibiotics abrogated these effects. FMT-PA and FMT-THMC activated autophagy and decreased IL-1β, IL-18, Wnt1, β-catenin, and TRPV1 expression. FMT-PA and FMT-THMC partially reversed the effects of 3-MA. Taken together, our data suggest that Yaobishu, PA, and THMC relieve inflammation and pain by remodeling the gut microbiota and restoring metabolic homeostasis after LDH to activate autophagy and the Wnt/β-catenin pathway, which provide a new therapeutic target for LDH in the clinic.}, }
@article {pmid38016486, year = {2023}, author = {Chen, H and Peng, L and Wang, Z and He, Y and Zhang, X}, title = {Exploring the causal relationship between periodontitis and gut microbiome: Unveiling the oral-gut and gut-oral axes through bidirectional Mendelian randomization.}, journal = {Journal of clinical periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jcpe.13906}, pmid = {38016486}, issn = {1600-051X}, support = {CSTB2022NSCQ-MSX0084//the Natural Science Foundation Project of Chongqing, China/ ; 81700982//National Natural Science Foundation of China/ ; ZQNYXGDRCGZS2019004//the Chongqing Medical Reserve Talent Studio for Young People/ ; }, abstract = {AIM: This Mendelian randomization (MR) study was performed to explore the potential bidirectional causal relationship between the gut microbiome (GM) and periodontitis.<br><br>MATERIALS AND METHODS: We used genetic instruments from the genome-wide association study of European descent for periodontitis from the GeneLifestyle Interactions in Dental Endpoints (GLIDE) consortium (17,353 cases and 28,210 controls) and the FinnGen consortium (4434 cases and 259,234 controls) to investigate the causal relationship with GM (the MiBioGen consortium, 18,340 samples), and vice versa. Several MR techniques, which include inverse variance weighting (IVW), MR-Egger, weighted median, simple mode and weighted mode approaches, were employed to investigate the causal relationship between the exposures and the outcomes. Cochran's Q-test was performed to detect heterogeneity. The MR-Egger regression intercept and MR pleiotropy residual sum and outlier test (MR-PRESSO) were conducted to test potential horizontal pleiotropy. Leave-one-out sensitivity analyses were used to assess the stabilities of single nucleotide polymorphisms (SNPs). Finally, the IVW results from the two databases were analysed using meta-analysis.<br><br>RESULTS: We confirmed three potential causal relationships between GM taxa and periodontitis at the genus level. Among them, the genera Alistipes and Holdemanella were genetically associated with an increased risk of periodontitis. In reverse, periodontitis may lead to a decreased abundance of the genus Ruminococcaceae UCG014.<br><br>CONCLUSIONS: The demonstration of a causal link between GM and periodontitis provides compelling evidence, highlighting the interconnectivity and interdependence of the gut-oral and oral-gut axes.}, }
@article {pmid38016408, year = {2023}, author = {Li, J and Li, Y and Xiao, H and Li, W and Ye, F and Wang, L and Li, Y and Wang, C and Wu, Y and Xuan, R and Huang, Y and Huang, J}, title = {The intestinal microflora diversity of aboriginal chickens in Jiangxi province, China.}, journal = {Poultry science}, volume = {103}, number = {2}, pages = {103198}, doi = {10.1016/j.psj.2023.103198}, pmid = {38016408}, issn = {1525-3171}, abstract = {Intestinal microbiota can coevolve with host to form symbiotic relationship and be participated in the regulation of host physiological function. At present, there is no clear explanation on the effect of intestinal microflora in Jiangxi aboriginal chickens. Here, we investigated the association between gut microbiota and host genome of Jiangxi local chickens using 16S rRNA sequencing and genome-wide association studies (GWAS). The results showed that the breeds and genders had important effects on the intestinal microbiota of chickens. A total of 28 SNPs in 14 regions of the chicken genome were related to the relative abundance of microorganisms in 5 genera: Clostridium_sensu_stricto_1, Enterococcus, Gallibacterium, Turicibacter, and Rikenellaceae_RC9_gut_group. A total of 17 candidate genes were identified composition of chicken microbiome and show an association between the host genome and the chicken intestinal microbiota, which also unveiled the diversity of intestinal microbes in Jiangxi chickens. Given the correlation between chicken genome and intestinal microbe found in the present study, a new idea for the protection of aboriginal chicken genetic resources in China could be provided.}, }
@article {pmid38016379, year = {2023}, author = {Kavita,  and Om, H and Chand, U and Kushawaha, PK}, title = {Postbiotics: An alternative and innovative intervention for the therapy of inflammatory bowel disease.}, journal = {Microbiological research}, volume = {279}, number = {}, pages = {127550}, doi = {10.1016/j.micres.2023.127550}, pmid = {38016379}, issn = {1618-0623}, abstract = {Inflammatory Bowel Disease (IBD) is a persistent gastrointestinal (GI) tract inflammatory disease characterized by downregulated mucosal immune activities and a disrupted microbiota environment in the intestinal lumen. The involvement of bacterium postbiotics as mediators between the immune system and gut microbiome could be critical in determining why host-microbial relationships are disrupted in IBD. Postbiotics including Short-chain fatty acids (SCFAs), Organic acids, Proteins, Vitamins, Bacteriocins, and Tryptophan (Trp) are beneficial bioactive compounds formed via commensal microbiota in the gut environment during the fermentation process that can be used to improve consumer health. The use of metabolites or fragments from microorganisms can be a very attractive treatment and prevention technique in modern medicine. Postbiotics are essential in the immune system's development since they alter the barrier tightness, and the gut ecology and indirectly shape the microbiota's structure. As a result, postbiotics may be beneficial in treating or preventing various diseases, even some for which there is no effective causative medication. Postbiotics may be a promising tool for the treatment of IBD in individuals of all ages, genders, and even geographical locations. Direct distribution of postbiotics may provide a new frontier in microbiome-based therapy for IBD since it allows both the management of host homeostasis and the correction of the negative implications of dysbiosis. Further studies of the biological effects of these metabolites are expected to reveal innovative applications in medicine and beyond. This review attempts to explore the possible postbiotic-based interventions for the treatment of IBD.}, }
@article {pmid38016374, year = {2023}, author = {Wang, P and Zhang, S and Qi, C and Wang, C and Zhu, Z and Shi, L and Cheng, L and Zhang, X}, title = {Blood microbial analyses reveal long-term effects of SARS-CoV-2 infection on patients who recovered from COVID-19.}, journal = {Computers in biology and medicine}, volume = {168}, number = {}, pages = {107721}, doi = {10.1016/j.compbiomed.2023.107721}, pmid = {38016374}, issn = {1879-0534}, abstract = {OBJECTIVE: Few symptoms persist for a long time after patients recover from COVID-19, called "long COVID". We explored the potential microbial risk factors for COVID-19 for a deeper understanding and assistance in the follow-up treatment of these sequelae.<br><br>METHODS: Microbiome re-annotation was performed using whole blood RNA-Seq data collected from recovered COVID-19 patients and healthy controls at multiple time points. Subsequently, a series of downstream analyses were conducted to reveal the microbial characteristics of patients who recovered from SARS-CoV-2 infection.<br><br>RESULTS: The blood microbiome at 12 weeks post-infection was most evidently disturbed, including an increasing ratio of Bacillota/Bacteroidota and a higher microbial alpha diversity. In addition, a group of pathogenic microbes at 12 weeks post-infection were identified, including Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa, which were positively associated with host genes involved in immune regulatory and olfactory transduction pathways. Several microbes, such as Streptococcus pneumoniae were associated with infiltrating immune cells, such as M2 macrophages.<br><br>CONCLUSION: This study provides insights into the relationship between the blood microbiome and COVID-19 sequelae. Several pathogenic microbes were enriched in recovered COVID-19 patients and thus affected host genes participating in the immune and olfactory transduction pathways, which play critical roles in COVID-19 sequelae.}, }
@article {pmid38016319, year = {2023}, author = {Xu, H and Wang, J and Wang, Q and Tu, W and Jin, Y}, title = {Co-exposure to polystyrene microplastics and cypermethrin enhanced the effects on hepatic phospholipid metabolism and gut microbes in adult zebrafish.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133051}, doi = {10.1016/j.jhazmat.2023.133051}, pmid = {38016319}, issn = {1873-3336}, abstract = {Microplastics (MPs) can absorb environmental pollutants from the aquatic environment to cause mixed toxicity, which has received widespread attention. However, studies on the joint effects of MPs and insecticides are limited. As one of the most widely used pyrethroids, there was a large amount of residual cypermethrin (CYP) in water due to insufficient decomposition. Here, adult female zebrafish were exposed to MPs, CYP, and their mixtures for 21 days, respectively. After exposures, the MPs and CYP caused tissue damage to the liver. Hepatic triglyceride (TG) level increased significantly after MPs + CYP exposure, and the expression of genes about glycolipids metabolism was significantly altered. Furthermore, metabolome results suggested that MPs + CYP exposure resulted in increased content of some glycerophospholipid, affecting phospholipid metabolism-related pathways. In addition, through 16 s rDNA sequencing, it was found that MPs + CYP led to significant changes in the proportion of dominant phyla. Interestingly, Cetobacterium which increased in CYP and the co-exposure group was positively correlated with most lipid metabolites. Our results suggested that co-exposure to MPs and CYP enhanced the disturbances in hepatic phospholipid metabolism by affecting the gut microbial composition, while these changes were not observed in separate treatment groups. These results emphasized the importance of studying the joint toxicity of MPs and insecticides.}, }
@article {pmid38016315, year = {2023}, author = {Gao, FZ and He, LY and He, LX and Bai, H and Zhang, M and Chen, ZY and Qiao, LK and Liu, YS and Ying, GG}, title = {Swine farming shifted the gut antibiotic resistome of local people.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133082}, doi = {10.1016/j.jhazmat.2023.133082}, pmid = {38016315}, issn = {1873-3336}, abstract = {Antibiotic resistance genes (ARGs) are prevalent in the livestock environment, but little is known about impacts of animal farming on the gut antibiotic resistome of local people. Here we conducted metagenomic sequencing to investigate gut microbiome and resistome of residents in a swine farming village as well as environmental relevance by comparing with a nearby non-farming village. Results showed a shift of gut microbiome towards unhealthy status in the residents of swine farming village, with an increased abundance and diversity in pathogens and ARGs. The resistome composition in human guts was more similar with that in swine feces and air than that in soil and water. Mobile gene elements were closely associated with the prevalence of gut resistome. Some plasmid-borne ARGs were colocalized in similar genetic contexts in gut and environmental samples. Metagenomic binning obtained 47 ARGs-carrying families in human guts, and therein Enterobacteriaceae posed the highest threats in antibiotic resistance and virulence. Several ARGs-carrying families were shared by gut and environmental samples (mainly in swine feces and air), and the ARGs were evolutionarily conservative within genera. The findings highlight that swine farming can shape gut resistome of local people with close linkage to farm environmental exposures.}, }
@article {pmid38016313, year = {2023}, author = {Kim, MS and Lee, YH and Lee, Y and Jeong, H and Wang, M and Wang, DZ and Lee, JS}, title = {Multigenerational effects of elevated temperature on host-microbiota interactions in the marine water flea Diaphanosoma celebensis exposed to micro- and nanoplastics.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {132877}, doi = {10.1016/j.jhazmat.2023.132877}, pmid = {38016313}, issn = {1873-3336}, abstract = {Rising ocean temperatures are driving unprecedented changes in global marine ecosystems. Meanwhile, there is growing concern about microplastic and nanoplastic (MNP) contamination, which can endanger marine organisms. Increasing ocean warming (OW) and plastic pollution inevitably cause marine organisms to interact with MNPs, but relevant studies remain sparse. Here, we investigated the interplay between ocean warming and MNP in the marine water flea Diaphanosoma celebensis. We found that combined exposure to MNPs and OW induced reproductive failure in the F2 generation. In particular, the combined effects of OW and MNPs on the F2 generation were associated with key genes related to reproduction and stress response. Moreover, populations of predatory bacteria were significantly larger under OW and MNP conditions during F2 generations, suggesting a potential link between altered microbiota and host fitness. These results were supported by a host transcriptome and microbiota interaction analysis. This research sheds light on the complex interplay between environmental stressors, their multigenerational effects on marine organisms, and the function of the microbiome.}, }
@article {pmid38016224, year = {2023}, author = {Ke, Y and Sun, W and Xue, Y and Zhu, Y and Yan, S and Xie, S}, title = {Effects of treatments and distribution on microbiome and antibiotic resistome from source to tap water in three Chinese geographical regions based on metagenome assembly.}, journal = {Water research}, volume = {249}, number = {}, pages = {120894}, doi = {10.1016/j.watres.2023.120894}, pmid = {38016224}, issn = {1879-2448}, abstract = {Antibiotic resistance genes (ARGs) represent emerging environmental pollutants that present health risks. Drinking water supply systems (DWSSs), including sources to tap water, play crucial roles in the dissemination and propagation of ARGs. However, there was a paucity of knowledge on the relative abundance, diversity, mobility, and pathogenic hosts of ARGs in DWSSs from source to tap. Therefore, the effects of treatments and distributions on the microbial community and ARGs from three geographical regions (downstream areas of the Yellow, Yangtze, and Pearl Rivers) were elucidated in the present study. Treatment processes lowered the complexity of the microbial community network, whereas transportation increased it. The assembly mechanisms of the microbial community and antibiotic resistome were primarily driven by stochastic processes. Distribution greatly increased the contribution of stochastic processes. Multidrug ARGs (for example, multidrug transporter and adeJ) and bacitracin ARG (bacA) were the primary mobile ARGs in drinking water, as identified by the metagenomic assembly. Achromobacter xylosoxidans, Acinetobacter calcoaceticus, and Acinetobacter junii harbored diverse multidrug ARGs and mobile genetic elements (MGEs) (recombinases, integrases, and transposases) as potential pathogens and were abundant in the disinfected water. Environmental factors, including pH, chlorine, latitude, longitude, and temperature, influenced the ARG abundance by directly regulating the MGEs and microbial community diversity. This study provides critical information on the fate, mobility, host pathogenicity, and driving factors of ARGs in drinking water, which is conducive to ARG risk assessment and management to provide high-quality drinking water to consumers.}, }
@article {pmid38016221, year = {2023}, author = {Zhang, X and Wang, Y and Jiao, P and Zhang, M and Deng, Y and Jiang, C and Liu, XW and Lou, L and Li, Y and Zhang, XX and Ma, L}, title = {Microbiome-functionality in anaerobic digesters: A critical review.}, journal = {Water research}, volume = {249}, number = {}, pages = {120891}, doi = {10.1016/j.watres.2023.120891}, pmid = {38016221}, issn = {1879-2448}, abstract = {Microbially driven anaerobic digestion (AD) processes are of immense interest due to their role in the biovalorization of biowastes into renewable energy resources. The function-versatile microbiome, interspecies syntrophic interactions, and trophic-level metabolic pathways are important microbial components of AD. However, the lack of a comprehensive understanding of the process hampers efforts to improve AD efficiency. This study presents a holistic review of research on the microbial and metabolic "black box" of AD processes. Recent research on microbiology, functional traits, and metabolic pathways in AD, as well as the responses of functional microbiota and metabolic capabilities to optimization strategies are reviewed. The diverse ecophysiological traits and cooperation/competition interactions of the functional guilds and the biomanipulation of microbial ecology to generate valuable products other than methane during AD are outlined. The results show that AD communities prioritize cooperation to improve functional redundancy, and the dominance of specific microbes can be explained by thermodynamics, resource allocation models, and metabolic division of labor during cross-feeding. In addition, the multi-omics approaches used to decipher the ecological principles of AD consortia are summarized in detail. Lastly, future microbial research and engineering applications of AD are proposed. This review presents an in-depth understanding of microbiome-functionality mechanisms of AD and provides critical guidance for the directional and efficient bioconversion of biowastes into methane and other valuable products.}, }
@article {pmid38016191, year = {2023}, author = {Zhang, Y and Zhan, J and Ma, C and Liu, W and Huang, H and Yu, H and Christie, P and Li, T and Wu, L}, title = {Root-associated bacterial microbiome shaped by root selective effects benefits phytostabilization by Athyrium wardii (Hook.).}, journal = {Ecotoxicology and environmental safety}, volume = {269}, number = {}, pages = {115739}, doi = {10.1016/j.ecoenv.2023.115739}, pmid = {38016191}, issn = {1090-2414}, abstract = {The root-associated microbiome assembly substantially promotes (hyper)accumulator plant growth and metal accumulation and is influenced by multiple factors, especially host species and environmental stress. Athyrium wardii (Hook.) is a phytostabilizer that grows in lead (Pb)-zinc (Zn) mine tailings and shows high root Pb accumulation. However, there remains little information on the assembly of the root-associated microbiome of A. wardii and its role in phytostabilization. A field study investigated the structural and functional variation in the root-associated bacterial microbiome of Athyrium wardii (Hook.) exposed to different levels of contamination in Pb-Zn mine tailings. The root compartment dominated the variation in the root-associated bacterial microbiome but the levels of contaminants showed less impact. Bacterial co-occurrence was enhanced in the rhizosphere soil and rhizoplane but tended to be much simpler in the endosphere in terms of network complexity and connectivity. This indicates that the microbial community assembly of A. wardii was non-random and shaped by root selective effects. Proteobacteria, Chloroflexi, Actinobacteria, Cyanobacteria, and Acidobacteriota were generally the dominant bacterial phyla. The genera Crossiella and Bradyrhizobium were enriched in the rhizosphere and cyanobacterial genera were enriched in the endosphere, demonstrating substantial advantages to plant survival and adaptation in the harsh mine environment. Functional categories involved in amino acid and carbohydrate metabolism were abundant in the rhizosphere soil, thus contributing to metal solubility and bioavailability in the rhizosphere. Membrane transporters, especially ATP-binding cassette transporters, were enriched in the endosphere, indicating a potential role in metal tolerance and transportation in A. wardii. The study shows substantial variation in the structure and function of microbiomes colonizing different compartments, with the rhizosphere and endophytic microbiota potentially involved in plant metal tolerance and accumulation during phytostabilization.}, }
@article {pmid38016054, year = {2023}, author = {Ilinskaya, ON and Gafarova, LF and Kurdy, W and Kolpakov, AI and Yakovleva, GY}, title = {[Microbiome of therapeutic muds used in Tatarstan].}, journal = {Voprosy kurortologii, fizioterapii, i lechebnoi fizicheskoi kultury}, volume = {100}, number = {5}, pages = {27-35}, doi = {10.17116/kurort202310005127}, pmid = {38016054}, issn = {0042-8787}, abstract = {UNLABELLED: Therapeutic muds (peloids), which are widely used for body healing, improve metabolism and have antibacterial, anti-inflammatory and analgesic effects due to enrichment with necessary microelements and biological active substances. However, the microbiological component of these effects is not well studied.<br><br>OBJECTIVE: To characterize the microbiome of therapeutic muds, used in the Tatarstan Republic, by identifying spectrum of cultivated microorganisms, using molecular analysis of bacterial communities, and by determining their biodiversity and functional potential based on revealed genetic determinants.<br><br>MATERIAL AND METHODS: The study design of 5 peloids samples (local sapropels and peat deposits of swamp; 3 samples of Crimean sulfide muds) included three main techniques: isolation and taxonomic determination of cultivated microorganisms by time-of-flight mass-spectrometry; molecular analysis of peloids bacterial communities by 16S RNA high-throughput sequencing; identification of functional profiles of communities by their genetic determinant using Global Mapper tool on iVikodak platform.<br><br>RESULTS: Experimental studies have confirmed the safety of examined peloids, where non-pathogenic cultivated bacteria belonging mainly to Bacillus and Rhodococcus genera were dominant. Metagenomic analysis showed that Firmicutes, Proteobacteria and Actinobacteria were predominant in all samples in different ratios. It has been established, that there is both the internal biodiversity of each sample and difference between them. The functional profile of microbial communities was determined based on the identification of bacterial genes. It has been revealed that all communities have an ability to synthesize antibiotics, as well as to decompose dangerous xenobiotics - polyaromatic hydrocarbons, cyclic compounds, and dioxins.<br><br>CONCLUSION: Various microbial communities, which were identified in the therapeutic muds, contribute both to the clearance of toxicants in the peloids and to the antibacterial properties of the latter. The obtained priority results create a fundamental basis for the subsequent study of the role of peloids' microbiome of different origin in their healing action.}, }
@article {pmid38015769, year = {2023}, author = {Najmanová, L and Vídeňská, P and Cahová, M}, title = {Corrigendum for: Healthy Microbiome - a Mere Idea or a Sound Concept?.}, journal = {Physiological research}, volume = {72}, number = {5}, pages = {684}, pmid = {38015769}, issn = {1802-9973}, abstract = {List of changes: On the basis of author's request the publisher of Physiological Research decided to change the license of the article to CC BY license.}, }
@article {pmid38015713, year = {2023}, author = {Agrawal, P and Kaur, J and Singh, J and Rasane, P and Sharma, K and Bhadariya, V and Kaur, S and Kumar, V}, title = {Genetics, Nutrition, and Health: A New Frontier in Disease Prevention.}, journal = {Journal of the American Nutrition Association}, volume = {}, number = {}, pages = {1-13}, doi = {10.1080/27697061.2023.2284997}, pmid = {38015713}, issn = {2769-707X}, abstract = {The field of nutrition research has traditionally focused on the effects of macronutrients and micronutrients on the body. However, it has become evident that individuals have unique genetic makeups that influence their response to food. Nutritional genomics, which includes nutrigenetics and nutrigenomics, explores the interaction between an individual's genetic makeup, diet, and health outcomes. Nutrigenetics studies the impact of genetic variation on an individual's response to dietary nutrients, while nutrigenomics investigates how dietary components affect gene regulation and expression. These disciplines seek to understand the impact of diet on the genome, transcriptome, proteome, and metabolome. It provides insights into the mechanisms underlying the effect of diet on gene expression. Nutrients can cause the modification of genetic expression through epigenetic changes, such as DNA methylation and histone modifications. The aim of nutrigenomics is to create personalized diets based on the unique metabolic profile of an individual, gut microbiome, and genetic makeup to prevent diseases and promote health. Nutrigenomics has the potential to revolutionize the field of nutrition by combining the practicality of personalized nutrition with knowledge of genetic factors underlying health and disease. Thus, nutrigenomics offers a promising approach to improving health outcomes (in terms of disease prevention) through personalized nutrition strategies based on an individual's genetic and metabolic characteristics.}, }
@article {pmid38015634, year = {2023}, author = {Gurczynski, SJ and Lipinski, JH and Strauss, JY and Alam, S and Huffnagle, GB and Ranjan, P and Kennedy, LH and Moore, BB and O'Dwyer, DN}, title = {Horizontal transmission of gut microbiota attenuates mortality in lung fibrosis.}, journal = {JCI insight}, volume = {}, number = {}, pages = {}, doi = {10.1172/jci.insight.164572}, pmid = {38015634}, issn = {2379-3708}, abstract = {Pulmonary fibrosis is a chronic and often fatal disease. The pathogenesis is characterized by aberrant repair of lung parenchyma resulting in loss of physiological homeostasis, respiratory failure and death. The immune response in pulmonary fibrosis is dysregulated. The gut microbiome is a key regulator of immunity. The role of the gut microbiome in regulating the pulmonary immunity in lung fibrosis is poorly understood. Here, we determine the impact of gut microbiota on pulmonary fibrosis in C57BL/6 mice derived from different vendors (C57BL/6J and C57BL/6NCrl). We use germ free models, fecal microbiota transplantation and cohousing to transmit gut microbiota. Metagenomic studies of feces establish keystone species between sub-strains. Pulmonary fibrosis is microbiota dependent in C57BL/6 mice. Gut microbiota are distinct by β diversity (PERMANOVA P<0.001) and α diversity (P<0.0001). Mortality and lung fibrosis are attenuated in C57BL/6NCrl mice. Elevated CD4+ IL-10+ T cells and lower IL-6 occur in C57BL/6NCrl mice. Horizontal transmission of microbiota by cohousing attenuates mortality in C57BL/6J mice and promotes a transcriptionally altered pulmonary immunity. Temporal changes in lung and gut microbiota demonstrates that gut microbiota contribute largely to immunological phenotype. Key regulatory gut microbiota contribute to lung fibrosis generating rationale for human studies.}, }
@article {pmid38015339, year = {2023}, author = {Brar, B and Kumar, R and Sharma, D and Sharma, AK and Thakur, K and Mahajan, D and Kumar, R}, title = {Metagenomic analysis reveals diverse microbial community and potential functional roles in Baner rivulet, India.}, journal = {Journal, genetic engineering &amp; biotechnology}, volume = {21}, number = {1}, pages = {147}, pmid = {38015339}, issn = {2090-5920}, abstract = {BACKGROUND: The health index of any population is directly correlated with the water quality, which in turn depends upon physicochemical characteristics and the microbiome of that aquatic source. For maintaining the water quality, knowledge of microbial diversity is a must. The present investigation attempts to evaluate the microflora of Baner. Metagenomics has been proven to be the technique for examining the genetic diversity of unculturable microbiota without using traditional culturing techniques. The microbial profile of Baner is analyzed using metagenomics for the first time to the best of our knowledge.<br><br>RESULTS: To explore the microbial diversity of Baner, metagenomics analysis from 3 different sites was done. Data analysis identified 29 phyla, 62 classes, 131 orders, 268 families, and 741 genera. Proteobacteria was found to be the most abundant phylum in all the sampling sites, with the highest abundance at S3 sampling site (94%). Bacteroidetes phylum was found to be second abundant in S1 and S2 site, whereas Actinobacteria was second dominant in sampling site S3. Enterobacteriaceae family was dominant in site S1, whereas Comamonadaceae and Pseudomonadaceae was abundant in sites S2 and S3 respectively. The Baner possesses an abundant bacterial profile that holds great promise for developing bioremediation tactics against a variety of harmful substances.<br><br>CONCLUSION: Baner river's metagenomic analysis offers the first insight into the microbial profile of this hilly stream. Proteobacteria was found to be the most abundant phylum in all the sampling sites indicating anthropogenic interference and sewage contamination. The highest abundance of proteobacteria at S3 reveals it to be the most polluted site, as it is the last sampling site downstream of the area under investigation, and falls after crossing the main city, so more human intervention and pollution were observed. Despite some pathogens, a rich profile of bacteria involved in bioremediation, xenobiotic degradation, and beneficial fish probiotics was observed, reflecting their potential applications for improving water quality and establishing a healthy aquaculture and fishery section.}, }
@article {pmid38015302, year = {2023}, author = {Kavyani, B and Ahn, SB and Missailidis, D and Annesley, SJ and Fisher, PR and Schloeffel, R and Guillemin, GJ and Lovejoy, DB and Heng, B}, title = {Dysregulation of the Kynurenine Pathway, Cytokine Expression Pattern, and Proteomics Profile Link to Symptomology in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS).}, journal = {Molecular neurobiology}, volume = {}, number = {}, pages = {}, pmid = {38015302}, issn = {1559-1182}, abstract = {Dysregulation of the kynurenine pathway (KP) is believed to play a significant role in neurodegenerative and cognitive disorders. While some evidence links the KP to myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), further studies are needed to clarify the overall picture of how inflammation-driven KP disturbances may contribute to symptomology in ME/CFS. Here, we report that plasma levels of most bioactive KP metabolites differed significantly between ME/CFS patients and healthy controls in a manner consistent with their known contribution to symptomology in other neurological disorders. Importantly, we found that enhanced production of the first KP metabolite, kynurenine (KYN), correlated with symptom severity, highlighting the relationship between inflammation, KP dysregulation, and ME/CFS symptomology. Other significant changes in the KP included lower levels of the downstream KP metabolites 3-HK, 3-HAA, QUIN, and PIC that could negatively impact cellular energetics. We also rationalized KP dysregulation to changes in the expression of inflammatory cytokines and, for the first time, assessed levels of the iron (Fe)-regulating hormone hepcidin that is also inflammation-responsive. Levels of hepcidin in ME/CFS decreased nearly by half, which might reflect systemic low Fe levels or possibly ongoing hypoxia. We next performed a proteomics screen to survey for other significant differences in protein expression in ME/CFS. Interestingly, out of the seven most significantly modulated proteins in ME/CFS patient plasma, 5 proteins have roles in maintaining gut health, which considering the new appreciation of how gut microbiome and health modulates systemic KP could highlight a new explanation of symptomology in ME/CFS patients and potential new prognostic biomarker/s and/or treatment avenues.}, }
@article {pmid38015063, year = {2023}, author = {Zhu, R and Gao, Y and Dong, J and Li, Z and Ren, Z}, title = {The changes of gut microbiota and metabolites in different drug-induced liver injuries.}, journal = {Journal of medical microbiology}, volume = {72}, number = {11}, pages = {}, doi = {10.1099/jmm.0.001778}, pmid = {38015063}, issn = {1473-5644}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Chemical and Drug Induced Liver Injury ; Multiomics ; }, abstract = {The increasing incidence of drug-induced liver injury (DILI) has become a major concern. Gut microbiota, as another organ of the human body, has been studied in various tumors, cardiovascular metabolic diseases, inflammatory bowel disease and human immunity. The studies mentioned above have confirmed its important impact on the occurrence and development of DILI. The gut-liver axis explains the close relationship between the gut and the liver, and it may be a pathway by which gut microbes contribute to DILI. In addition, the interaction between drugs and gut microbes affects both separately, which in turn may have positive or negative effects on the body, including DILI. There are both common and specific changes in liver injury caused by different drugs. The alteration of metabolites in DILI is also a new direction of therapeutic exploration. The application of microbiomics, metabolomics and other multi-omics to DILI has also explored new ideas for DILI. In this review, we conclude the alterations of gut microbes and metabolites under different DILI, and the significance of applying gut microbiome-metabolomics to DILI, so as to explore the metabolic characteristics of DILI and possible novel metabolic biomarkers.}, }
@article {pmid38014976, year = {2023}, author = {Zhuang, Y and Guo, W and Cui, K and Tu, Y and Diao, Q and Zhang, N and Bi, Y and Ma, T}, title = {Altered microbiota, antimicrobial resistance genes, and functional enzyme profiles in the rumen of yak calves fed with milk replacer.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0131423}, doi = {10.1128/spectrum.01314-23}, pmid = {38014976}, issn = {2165-0497}, abstract = {Yaks, as ruminants inhabiting high-altitude environments, possess a distinct rumen microbiome and are resistant to extreme living conditions. This study investigated the microbiota, resistome, and functional gene profiles in the rumen of yaks fed milk or milk replacer (MR), providing insights into the regulation of the rumen microbiome and the intervention of antimicrobial resistance in yaks through dietary methods. The abundance of Prevotella members increased significantly in response to MR. Tetracycline resistance was the most predominant. The rumen of yaks contained multiple antimicrobial resistance genes (ARGs) originating from different bacteria, which could be driven by MR, and these ARGs displayed intricate and complex interactions. MR also induced changes in functional genes. The enzymes associated with fiber degradation and butyrate metabolism were activated and showed close correlations with Prevotella members and butyrate concentration. This study allows us to deeply understand the ruminal microbiome and ARGs of yaks and their relationship with rumen bacteria in response to different milk sources.}, }
@article {pmid38014962, year = {2023}, author = {Ren, W and Penttilä, R and Kasanen, R and Asiegbu, FO}, title = {Interkingdom and intrakingdom interactions in the microbiome of Heterobasidion fruiting body and associated decayed woody tissues.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0140623}, doi = {10.1128/aem.01406-23}, pmid = {38014962}, issn = {1098-5336}, abstract = {We applied macro- (forest stand and forest management) and micro-scale (bacterial and fungal community) analyses for a better understanding of the Heterobasidion pathosystem and associated wood decay process. The core microbiome, as defined by hierarchy analysis and a consistent model, and environmental factors correlation with the community assembly were found to be novel.}, }
@article {pmid38014951, year = {2023}, author = {LaReau, JC and Hyde, J and Brackney, DE and Steven, B}, title = {Introducing an environmental microbiome to axenic Aedes aegypti mosquitoes documents bacterial responses to a blood meal.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0095923}, doi = {10.1128/aem.00959-23}, pmid = {38014951}, issn = {1098-5336}, abstract = {The blood meal of the female mosquito serves as a nutrition source to support egg development, so is an important aspect of its biology. Yet, the roles the microbiome may play in blood digestion are poorly characterized. We employed axenic mosquitoes to investigate how the microbiome differs between mosquitoes reared in the insectary versus mosquitoes that acquire their microbiome from the environment. Environmental microbiomes were more diverse and showed larger temporal shifts over the course of blood digestion. Importantly, only bacteria from the environmental microbiome performed hemolysis in culture, pointing to functional differences between bacterial populations. These data highlight that taxonomic differences between the microbiomes of insectary-reared and wild mosquitoes are potentially also related to their functional ecology. Thus, axenic mosquitoes colonized with environmental bacteria offer a way to investigate the role of bacteria from the wild in mosquito processes such as blood digestion, under controlled laboratory conditions.}, }
@article {pmid38014935, year = {2023}, author = {Shimpi, GG and De la Vega, P and Bentlage, B}, title = {Complete genome sequence of Brachybacterium sp. GU-2 (Actinomycetota), isolated from the massive coral Porites lobata.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0085523}, doi = {10.1128/MRA.00855-23}, pmid = {38014935}, issn = {2576-098X}, abstract = {Brachybacterium sp. GU-2 was isolated from the hard coral Porites lobata found in Apra Harbor, Guam, Micronesia. This genome sequence will be beneficial to understand the role of actinomycetes in coral holobionts. The Brachybacterium genome contains several gene clusters for bioactive compounds, including antibiotics.}, }
@article {pmid38014746, year = {2023}, author = {Fountain-Jones, NM and Giraud, T and Zinger, L and Bik, H and Creer, S and Videvall, E}, title = {Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.17223}, pmid = {38014746}, issn = {1365-294X}, abstract = {The study of microbiomes across organisms and environments has become a prominent focus in molecular ecology. This perspective article explores common challenges, methodological advancements, and future directions in the field. Key research areas include understanding the drivers of microbiome community assembly, linking microbiome composition to host genetics, exploring microbial functions, transience and spatial partitioning, and disentangling non-bacterial components of the microbiome. Methodological advancements, such as quantifying absolute abundances, sequencing complete genomes, and utilizing novel statistical approaches, are also useful tools for understanding complex microbial diversity patterns. Our aims are to encourage robust practices in microbiome studies and inspire researchers to explore the next frontier of this rapidly changing field.}, }
@article {pmid38014621, year = {2023}, author = {Romberg, N and Le Coz, C}, title = {Common variable immunodeficiency, cross currents, and prevailing winds.}, journal = {Immunological reviews}, volume = {}, number = {}, pages = {}, doi = {10.1111/imr.13291}, pmid = {38014621}, issn = {1600-065X}, support = {//Jeffrey Modell Foundation/ ; }, abstract = {Common variable immunodeficiency (CVID) is a heterogenous disease category created to distinguish late-onset antibody deficiencies from early-onset diseases like agammaglobulinemia or more expansively dysfunctional combined immunodeficiencies. Opinions vary on which affected patients should receive a CVID diagnosis which confuses clinicians and erects reproducibility barriers for researchers. Most experts agree that CVID's most indeliable feature is defective germinal center (GC) production of isotype-switched, affinity-maturated antibodies. Here, we review the biological factors contributing to CVID-associated GC dysfunction including genetic, epigenetic, tolerogenic, microbiome, and regulatory abnormalities. We also discuss the consequences of these biological phenomena to the development of non-infectious disease complications. Finally, we opine on topics and lines of investigation we think hold promise for expanding our mechanistic understanding of this protean condition and for improving the lives of affected patients.}, }
@article {pmid38014521, year = {2023}, author = {Du, C and Zuo, F and Cao, Y and Zang, Y}, title = {Anti-diabetic effects of natural and modified 'Ganzhou' navel orange peel pectin on type 2 diabetic mice via gut microbiota.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d3fo04118b}, pmid = {38014521}, issn = {2042-650X}, abstract = {Pectin, a kind of dietary fiber, has attracted much attention owing to its beneficial effect on human health in recent years. In this study, the effects of both 'Ganzhou' navel orange peel pectin (GOP) and modified GOP (MGOP) on type 2 diabetes (T2DM) were investigated. The results indicated that GOP and MGOP intervention had positive effects on T2DM in C57BL/6 mice. After modification, pectin can be changed into low methoxy pectin (LMP) and the content of GalA can increase, which endow MGOP with significant effects on improving lipid metabolism (TC, TG, and LDL-C decreased by 30.46%, 50%, and 37.56%, respectively, and HDL-C increased by 56%) and OGTT, further reducing insulin resistance (insulin decreased by 74.35%). In addition, MGOP was superior to GOP in improving oxidative stress (GSH and GSH-Px increased by 52.05% and 29.08% respectively, and MDA decreased by 84.02%), inhibiting inflammation and promoting SCFA synthesis. 16S rRNA analysis showed that MGOP changed the composition of intestinal microbiota in diabetic mice, decreased the abundance of Alistipes, Helicobacter and Oscillibacter, and increased the relative abundance of Dubosiella, Akkermansiaceae, and Atopobiaceae. The phenotypes of the gut microbiome also changed accordingly, which showed that MGOP significantly inhibited the growth of Gram-negative bacteria and potential pathogenic bacteria and reversed the related complications. Taken together, our findings revealed that MGOP intake regulated lipid metabolism and oxidative stress and improved the gut health of mice, with promising effects against T2DM and related complications.}, }
@article {pmid38014449, year = {2023}, author = {Engevik, MA and Thapa, S and Lillie, I and Yacyshyn, MB and Yacyshyn, B and Percy, AJ and Chace, D and Horvath, TD}, title = {Repurposing dried blood spot (DBS) device technology to examine bile acid profiles in human dried fecal spot (DFS) samples.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpgi.00188.2023}, pmid = {38014449}, issn = {1522-1547}, support = {K01K123195-01//HHS | NIH | NIDDK | Division of Diabetes, Endocrinology, and Metabolic Diseases (DEM)/ ; }, abstract = {Dried blood spot (DBS) analysis has existed for >50 years, but application of this technique to fecal analysis remains limited. To address whether dried fecal spots (DFS) could be used to measure fecal bile acids, we collected feces from five subjects for each of the following cohorts: i) healthy individuals, ii) individuals with diarrhea, and iii) Clostridioides difficile-infected patients. Homogenized fecal extracts were loaded onto quantitative DBS (qDBS) devices, dried overnight, and shipped to the bioanalytical lab at ambient temperature. For comparison, source fecal extracts were shipped on dry ice and stored frozen. After four months, frozen fecal extracts and ambient DFS samples were processed and subjected to targeted LC-MS/MS-based metabolomics with stable isotope-labeled standards. We observed no differences in the bile acid levels measured between the traditional extraction and the qDBS-based DFS methods. This pilot data demonstrate that DFS-based analysis is feasible and warrants further development for fecal compounds and microbiome applications.}, }
@article {pmid38014294, year = {2023}, author = {Pereira, FC and Ge, X and Kristensen, JM and Kirkegaard, RH and Maritsch, K and Zhu, Y and Decorte, M and Hausmann, B and Berry, D and Wasmund, K and Schintlmeister, A and Boettcher, T and Cheng, JX and Wagner, M}, title = {The Parkinson's drug entacapone disrupts gut microbiome homeostasis via iron sequestration.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.11.12.566429}, pmid = {38014294}, abstract = {Increasing evidence shows that many human-targeted drugs alter the gut microbiome, leading to implications for host health. However, much less is known about the mechanisms by which drugs target the microbiome and how drugs affect microbial function. Here we combined quantitative microbiome profiling, long-read metagenomics, stable isotope probing and single cell chemical imaging to investigate the impact of two widely prescribed nervous system targeted drugs on the gut microbiome. Ex vivo supplementation of physiologically relevant concentrations of entacapone or loxapine succinate to faecal samples significantly impacted the abundance of up to one third of the microbial species present. Importantly, we demonstrate that the impact of these drugs on microbial metabolism is much more pronounced than their impact on abundances, with low concentrations of drugs reducing the activity, but not the abundance of key microbiome members like Bacteroides, Ruminococcus or Clostridium species. We further demonstrate that entacapone impacts the microbiome due to its ability to complex and deplete available iron, and that microbial growth can be rescued by replenishing levels of microbiota-accessible iron. Remarkably, entacapone-induced iron starvation selected for iron-scavenging organisms carrying antimicrobial resistance and virulence genes. Collectively, our study unveils the impact of two under-investigated drugs on whole microbiomes and identifies metal sequestration as a mechanism of drug-induced microbiome disturbance.}, }
@article {pmid38014241, year = {2023}, author = {Frith, ME and Kashyap, PC and Linden, DR and Theriault, B and Chang, EB}, title = {Microbiota-dependent early life programming of gastrointestinal motility.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.11.08.566304}, pmid = {38014241}, abstract = {Gastrointestinal microbes modulate peristalsis and stimulate the enteric nervous system (ENS), whose development, as in the central nervous system (CNS), continues into the murine postweaning period. Given that adult CNS function depends on stimuli received during critical periods of postnatal development, we hypothesized that adult ENS function, namely motility, depends on microbial stimuli during similar critical periods. We gave fecal microbiota transplantation (FMT) to germ-free mice at weaning or as adults and found that only the mice given FMT at weaning recovered normal transit, while those given FMT as adults showed limited improvements. RNAseq of colonic muscularis propria revealed enrichments in neuron developmental pathways in mice exposed to gut microbes earlier in life, while mice exposed later - or not at all - showed exaggerated expression of inflammatory pathways. These findings highlight a microbiota-dependent sensitive period in ENS development, pointing to potential roles of the early life microbiome in later life dysmotility.}, }
@article {pmid38014162, year = {2023}, author = {Subramanian, P and Romero-Soto, HN and Stern, DB and Maxwell, GL and Levy, S and Hourigan, SK}, title = {Delivery mode impacts gut bacteriophage colonization during infancy.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.11.13.23298307}, pmid = {38014162}, abstract = {BACKGROUND: Cesarean section delivery is associated with altered early-life bacterial colonization and later adverse inflammatory and immune health outcomes. Although gut bacteriophages can alter gut microbiome composition and impact host immune responses, little is known about how delivery mode impacts bacteriophage colonization over time. To begin to address this we examined how delivery mode affected bacteriophage colonization over the first two years of life.<br><br>RESULTS: Shotgun metagenomic sequencing was conducted on 272 serial stool samples from 55 infants, collected at 1-2 days of life and 2, 6, 12 and 24 months. 33/55 (60%) infants were born by vaginal delivery. DNA viruses were identified, and by host inference, 94% of the viral sequences were found to be bacteriophages. Alpha diversity of the virome was increased in vaginally delivered infants compared to cesarean section delivered infants at 2 months (Shannon index, p=0.022). Beta diversity significantly differed by delivery mode at 2, 6, and 12 months when stratified by peripartum antibiotic use (Bray-Curtis dissimilarity, all p<0.05). Significant differentially abundant predicted bacteriophage hosts by delivery mode were seen at all time points. Moreover, there were differences in predicted bacteriophage functional gene abundances up to 24 months by delivery mode. Many of the functions considered to play a role in host response were increased in vaginal delivery.<br><br>CONCLUSIONS: Clear differences in bacteriophage composition and function were seen by delivery mode over the first two years of life. Given that phages are known to affect host immune response, our results suggest that future investigation into how delivery mode may lead to adverse inflammatory outcomes should not only include bacterial microbial colonization but also the potential role of bacteriophages and transkingdom interactions.}, }
@article {pmid38014088, year = {2023}, author = {Gundogan, K and Nellis, MM and Ozer, NT and Ergul, SS and Sahin, GG and Temel, S and Yuksel, RC and Teeny, S and Alvarez, JA and Sungur, M and Jones, DP and Ziegler, TR}, title = {High-Resolution Plasma Metabolomics and Thiamine Status in Critically Ill Adult Patients.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-3597052/v1}, pmid = {38014088}, abstract = {Thiamine (Vitamin B1) is an essential micronutrient and a co-factor for metabolic functions related to energy metabolism. We determined the association between whole blood thiamine pyrophosphate (TPP) concentrations and plasma metabolites using high resolution metabolomics in critically ill patients. Methods Cross-sectional study performed in Erciyes University Hospital, Kayseri, Turkey and Emory University, Atlanta, GA, USA. Participants were ≥ 18 years of age, with an expected length of ICU stay longer than 48 hours, receiving furosemide therapy for at least 6 months before ICU admission. Results Blood for TPP and metabolomics was obtained on the day of ICU admission. Whole blood TPP concentrations were measured using high-performance liquid chromatography (HPLC). Liquid chromatography/mass spectrometry was used for plasma high-resolution metabolomics. Data was analyzed using regression analysis of TPP levels against all plasma metabolomic features in metabolome-wide association studies. We also compared metabolomic features from patients in the highest TPP concentration tertile to patients in the lowest TPP tertile as a secondary analysis. We enrolled 76 participants with a median age of 69 (range, 62.5-79.5) years. Specific metabolic pathways associated with whole blood TPP levels, using both regression and tertile analysis, included pentose phosphate, fructose and mannose, branched chain amino acid, arginine and proline, linoleate, and butanoate pathways. Conclusions Plasma high-resolution metabolomics analysis showed that whole blood TPP concentrations are significantly associated with metabolites and metabolic pathways linked to the metabolism of energy, amino acids, lipids, and the gut microbiome in adult critically ill patients.}, }
@article {pmid38014044, year = {2023}, author = {Elovitz, M and Anton, L and Cristancho, A and Ferguson, B and Joseph, A and Ravel, J}, title = {Vaginal microbes alter epithelial transcriptomic and epigenomic modifications providing insight into the molecular mechanisms for susceptibility to adverse reproductive outcomes.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-3580132/v1}, pmid = {38014044}, abstract = {The cervicovaginal microbiome is highly associated with women's health with microbial communities dominated by Lactobacillus spp. being considered optimal. Conversely, a lack of lactobacilli and a high abundance of strict and facultative anaerobes including Gardnerella vaginalis , have been associated with adverse reproductive outcomes. However, the molecular pathways modulated by microbe interactions with the cervicovaginal epithelia remain unclear. Using RNA-sequencing, we characterize the in vitro cervicovaginal epithelial transcriptional response to different vaginal bacteria and their culture supernatants. We showed that G. vaginalis upregulated genes were associated with an activated innate immune response including anti-microbial peptides and inflammasome pathways, represented by NLRP3-mediated increases in caspase-1, IL-1β and cell death. Cervicovaginal epithelial cells exposed to L. crispatus showed limited transcriptomic changes, while exposure to L. crispatus culture supernatants resulted in a shift in the epigenomic landscape of cervical epithelial cells. ATAC-sequencing confirmed epigenetic changes with reduced chromatin accessibility. This study reveals new insight into host-microbe interactions in the lower reproductive tract and suggest potential therapeutic strategies leveraging the vaginal microbiome to improve reproductive health.}, }
@article {pmid38014043, year = {2023}, author = {Aparicio, A and Sun, Z and Gold, DR and Litonjua, AA and Weiss, ST and Lee-Sarwar, K and Liu, YY}, title = {Genotype-microbiome-metabolome associations in early childhood, and their link to BMI and childhood obesity.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.11.13.23298467}, pmid = {38014043}, abstract = {The influence of genotype on defining the human gut microbiome has been extensively studied, but definite conclusions have not yet been found. To fill this knowledge gap, we leverage data from children enrolled in the Vitamin D Antenatal Asthma Reduction Trial (VDAART) from 6 months to 8 years old. We focus on a pool of 12 genes previously found to be associated with the gut microbiome in independent studies, establishing a Bonferroni corrected significance level of p-value < 2.29 × 10 [-6] . We identified significant associations between SNPs in the FHIT gene (known to be associated with obesity and type 2 diabetes) and obesity-related microbiome features, and the children's BMI through their childhood. Based on these associations, we defined a set of SNPs of interest and a set of taxa of interest. Taking a multi-omics approach, we integrated plasma metabolome data into our analysis and found simultaneous associations among children's BMI, the SNPs of interest, and the taxa of interest, involving amino acids, lipids, nucleotides, and xenobiotics. Using our association results, we constructed a quadripartite graph where each disjoint node set represents SNPs in the FHIT gene, microbial taxa, plasma metabolites, or BMI measurements. Network analysis led to the discovery of patterns that identify several genetic variants, microbial taxa and metabolites as new potential markers for obesity, type 2 diabetes, or insulin resistance risk.}, }
@article {pmid38014007, year = {2023}, author = {Mah, JC and Lohmueller, KE and Garud, N}, title = {Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.11.09.566454}, pmid = {38014007}, abstract = {Despite the importance of gut commensal microbiota to human health, there is little knowledge about their evolutionary histories, including their population demographic histories and their distributions of fitness effects (DFE) of new mutations. Here, we infer the demographic histories and DFEs of 27 of the most highly prevalent and abundant commensal gut microbial species in North Americans over timescales exceeding human generations using a collection of lineages inferred from a panel of healthy hosts. We find overall reductions in genetic variation among commensal gut microbes sampled from a Western population relative to an African rural population. Additionally, some species in North American microbiomes display contractions in population size and others expansions, potentially occurring at several key historical moments in human history. DFEs across species vary from highly to mildly deleterious, with accessory genes experiencing more drift compared to core genes. Within genera, DFEs tend to be more congruent, reflective of underlying phylogenetic relationships. Taken together, these findings suggest that human commensal gut microbes have distinct evolutionary histories, possibly reflecting the unique roles of individual members of the microbiome.}, }
@article {pmid38013050, year = {2023}, author = {Okawa, Y and Sasagawa, S and Kato, H and Johnson, TA and Nagaoka, K and Kobayashi, Y and Hayashi, A and Shibayama, T and Maejima, K and Tanaka, H and Miyano, S and Shibahara, J and Nishizuka, S and Hirano, S and Seto, Y and Iwaya, T and Kakimi, K and Yasuda, T and Nakagawa, H}, title = {Immuno-genomic analysis reveals eosinophilic feature and favorable prognosis of female non-smoking esophageal squamous cell carcinomas.}, journal = {Cancer letters}, volume = {}, number = {}, pages = {216499}, doi = {10.1016/j.canlet.2023.216499}, pmid = {38013050}, issn = {1872-7980}, abstract = {Most of esophageal squamous cell carcinoma (ESCC) develop in smoking males in Japan, but the genomic etiology and immunological characteristics of rare non-smoking female ECSS remain unclear. To elucidate the genomic and immunological features of ESCC in non-smoking females, we analyzed whole-genome or transcriptome sequencing data from 94 ES CCs, including 20 rare non-smoking female cases. In addition, 31,611 immune cells were extracted from four ESCC tissues and subject to single-cell RNA-seq. We compared their immuno-genomic and microbiome profiles between non-smoking female and smoking ESCCs. Non-smoking females showed much better prognosis. Whole-genome sequencing analysis showed no significant differences in driver genes or copy number alterations depending on smoking status. The mutational signature specifically observed in non-smoking females ESCC could be attributed to aging. Immune profiling from RNA-seq revealed that ESCC in non-smoking females had high tumor microenvironment signatures and a high abundance of eosinophils with a favorable prognosis. Single-cell RNA-sequencing of intratumor immune cells revealed gender differences of eosinophils and their activation in female cases. ESCCs in non-smoking females have age-related mutational signatures and gender-specific tumor immune environment with eosinophils, which is likely to contribute to their favorable prognosis.}, }
@article {pmid38013035, year = {2023}, author = {Dong, W and Zhou, R and Li, X and Yan, H and Zheng, J and Peng, N and Zhao, S}, title = {Effect of simplified inoculum agent on performance and microbiome during cow manure-composting at industrial-scale.}, journal = {Bioresource technology}, volume = {393}, number = {}, pages = {130097}, doi = {10.1016/j.biortech.2023.130097}, pmid = {38013035}, issn = {1873-2976}, abstract = {A simplified inoculum agent, only comprising Bacillus subtilis and Aspergillus niger, was utilized for industrial-scale cow-manure composting to investigate its impact on composting performance and microbiome. Inoculants elevated the average and peak temperatures by up to 7 and 10 °C, respectively, during the thermophilic stage, reduced organic matter content, and raised germination index. Inoculation also extended the period of composting above 50 °C from 12 to 26 days. Sequencing unveiled significant shifts in microbial diversity, composition, and function. Aspergillus thrived during the mesophilic phase, potentially initiating composting, whereas Bacillus, Lysinibacillus, and Clostridium were enriched during the thermophilic stage. Metagenomic sequencing revealed an increased abundance of carbohydrate-active enzymes and glycometabolism-related genes responsible for lignocellulose degradation and heat generation after inoculation. These enriched microbes and functional genes contributed to organic matter degradation and temperature maintenance during thermophilic stage, expediting composting. This suggests the effectiveness of this simplified inoculum in industrial-level cow-manure composting.}, }
@article {pmid38012967, year = {2023}, author = {Zhao, J and Duan, G and Zhu, D and Li, J and Zhu, Y}, title = {Microbial-influenced pesticide removal co-occurs with antibiotic resistance gene variation in soil-earthworm-maize system.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {123010}, doi = {10.1016/j.envpol.2023.123010}, pmid = {38012967}, issn = {1873-6424}, abstract = {Within human-influenced landscapes, pesticides cooccur with a variety of antibiotic stressors. However, the relationship between pesticides removal process and antibiotic resistance gene variation are not well understood. This study explored pesticide (topramezone, TPZ) and antibiotic (polymyxin E, PME) co-contamination using liquid chromatography-tandem mass spectrometry (LC-MS/MS), bacterial-16 S rRNA sequencing and high-throughput quantitative polymerase chain reaction (HT-qPCR) in a soil-earthworm-maize system. After incubating soil for 28 days with TPZ and PME (10 mg kg[-1] dry weight), earthworm weight-gain, mortality rates, and maize plant weight-gain only differed slightly, but height-gain significantly decreased. PME significantly increased TPZ-removal in the soil. Accumulation of TPZ in earthworm's tissues may pose potential risks in the food chain. Combined pollution altered the microbial community structure and increased the abundance of functional microorganisms involved in aromatic compound degradation. Furthermore, maize rhizosphere can raise resistance genes, however earthworms can reduce resistance genes. Co-contamination increased absolute abundance of mobile genetic elements (MGEs) in bulk-soil samples, antibiotic resistance genes (ARGs) in skin samples and number of ARGs in bulk-soil samples, while decreased absolute abundance of transposase gene in bulk-soil samples and number of ARGs in rhizosphere-soil samples. Potential hosts harbouring ARGs may be associated with the antagonistic effect during resistance and detoxification of TPZ and PMB co-occurrence. These findings provide insights into the mechanism underlining pesticide removal regarding occurrence of ARGs in maize agroecosystem.}, }
@article {pmid38012609, year = {2023}, author = {Lai, TT and Liou, CW and Tsai, YH and Lin, YY and Wu, WL}, title = {Butterflies in the gut: the interplay between intestinal microbiota and stress.}, journal = {Journal of biomedical science}, volume = {30}, number = {1}, pages = {92}, pmid = {38012609}, issn = {1423-0127}, support = {112-2628-B-006-013-//National Science and Technology Council/ ; 110-2320-B-006-018-MY3//National Science and Technology Council/ ; 111-2314-B-006-008//National Science and Technology Council/ ; 110-2926-I-006-001-MY4//National Science and Technology Council/ ; 110-2314-B-006-114//Ministry of Science and Technology, Taiwan/ ; 109-2314-B-006-046//Ministry of Science and Technology, Taiwan/ ; 107-2320-B-006-072-MY3//Ministry of Science and Technology, Taiwan/ ; }, mesh = {Animals ; Humans ; *Gastrointestinal Microbiome ; *Butterflies ; }, abstract = {Psychological stress is a global issue that affects at least one-third of the population worldwide and increases the risk of numerous psychiatric disorders. Accumulating evidence suggests that the gut and its inhabiting microbes may regulate stress and stress-associated behavioral abnormalities. Hence, the objective of this review is to explore the causal relationships between the gut microbiota, stress, and behavior. Dysbiosis of the microbiome after stress exposure indicated microbial adaption to stressors. Strikingly, the hyperactivated stress signaling found in microbiota-deficient rodents can be normalized by microbiota-based treatments, suggesting that gut microbiota can actively modify the stress response. Microbiota can regulate stress response via intestinal glucocorticoids or autonomic nervous system. Several studies suggest that gut bacteria are involved in the direct modulation of steroid synthesis and metabolism. This review provides recent discoveries on the pathways by which gut microbes affect stress signaling and brain circuits and ultimately impact the host's complex behavior.}, }
@article {pmid38012587, year = {2023}, author = {Alyousef, YM and Piotrowski, S and Alonaizan, FA and Alsulaiman, A and Alali, AA and Almasood, NN and Vatte, C and Hamilton, L and Gandla, D and Lad, H and Robinson, FL and Cyrus, C and Meng, RC and Dowdell, A and Piening, B and Keating, BJ and Al-Ali, AK}, title = {Oral microbiota analyses of paediatric Saudi population reveals signatures of dental caries.}, journal = {BMC oral health}, volume = {23}, number = {1}, pages = {935}, pmid = {38012587}, issn = {1472-6831}, mesh = {Male ; Child ; Female ; Humans ; *Dental Caries/genetics ; Saudi Arabia ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Saliva ; }, abstract = {BACKGROUND: Oral microbiome sequencing has revealed key links between microbiome dysfunction and dental caries. However, these efforts have largely focused on Western populations, with few studies on the Middle Eastern communities. The current study aimed to identify the composition and abundance of the oral microbiota in saliva samples of children with different caries levels using machine learning approaches.<br><br>METHODS: Oral microbiota composition and abundance were identified in 250 Saudi participants with high dental caries and 150 with low dental caries using 16&#xa0;S rRNA sequencing on a NextSeq 2000 SP flow cell (Illumina, CA) using 250&#xa0;bp paired-end reads, and attempted to build a classifier using random forest models to assist in the early detection of caries.<br><br>RESULTS: The ADONIS test results indicate that there was no significant association between sex and Bray-Curtis dissimilarity (p&#x2009;~&#x2009;0.93), but there was a significant association with dental caries status (p&#x2009;~&#x2009;0.001). Using an alpha level of 0.05, five differentially abundant operational taxonomic units (OTUs) were identified between males and females as the main effect along with four differentially abundant OTUs between high and low dental caries. The mean metrics for the optimal hyperparameter combination using the model with only differentially abundant OTUs were: Accuracy (0.701); Matthew's correlation coefficient (0.0509); AUC (0.517) and F1 score (0.821) while the mean metrics for random forest model using all OTUs were:0.675; 0.054; 0.611 and 0.796 respectively.<br><br>CONCLUSION: The assessment of oral microbiota samples in a representative Saudi Arabian population for high and low metrics of dental caries yields signatures of abundances and diversity.}, }
@article {pmid38012477, year = {2023}, author = {Zhang, K and Ji, J and Li, N and Yin, Z and Fan, G}, title = {Integrated Metabolomics and Gut Microbiome Analysis Reveals the Efficacy of a Phytochemical Constituent in the Management of Ulcerative Colitis.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e2200578}, doi = {10.1002/mnfr.202200578}, pmid = {38012477}, issn = {1613-4133}, support = {2019KJ076//Tianjin Municipal Education Commission/ ; }, abstract = {SCOPE: Cinnamaldehyde (CAH), a phytochemical constituent isolated from cinnamon, is gaining attention due to its nutritional and medicinal benefits. This study aimed to investigate the potential role of CAH in the treatment of ulcerative colitis (UC).<br><br>METHODS AND RESULTS: Integrated metabolomics and gut microbiome analysis are performed for 2,4,6-trinitrobenzenesulfonic acid (TNBS) induced UC rats. The effect of CAH on colonic inflammation, lipid peroxidation, metabolic profiles, and gut microbiota is systematically explored. It finds that CAH improves the colitis-related symptoms, decreases disease activity index, increases the colon length and body weight, and alleviates histologic inflammation of UC rats. These therapeutic effects of CAH are due to suppression of inflammation and lipid peroxidation. Moreover, multi-omics analysis reveals that CAH treatment cause changes in plasma metabolome and gut microbiome in UC rats. CAH regulates lipid metabolic processes, especially phosphatidylcholines, lysophosphatidylcholines, and polyunsaturated fatty acids. Meanwhile, CAH modulates the gut microbial structure by restraining pathogenic bacteria (such as Helicobacter) and increasing probiotic bacteria (such as Bifidobacterium and Lactobacillus).<br><br>CONCLUSIONS: These results indicate that CAH exerts a beneficial role in UC by synergistic modulating the balance in gut microbiota and the associated metabolites, and highlights the nutritional and medicinal value of CAH in UC management.}, }
@article {pmid38012463, year = {2023}, author = {Hart, NH and Wallen, MP and Farley, MJ and Haywood, D and Boytar, AN and Secombe, K and Joseph, R and Chan, RJ and Kenkhuis, MF and Buffart, LM and Skinner, TL and Wardill, HR}, title = {Exercise and the gut microbiome: implications for supportive care in cancer.}, journal = {Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer}, volume = {31}, number = {12}, pages = {724}, pmid = {38012463}, issn = {1433-7339}, abstract = {PURPOSE: Growing recognition of the gut microbiome as an influential modulator of cancer treatment efficacy and toxicity has led to the emergence of clinical interventions targeting the microbiome to enhance cancer and health outcomes. The highly modifiable nature of microbiota to endogenous, exogenous, and environmental inputs enables interventions to promote resilience of the gut microbiome that have rapid effects on host health, or response to cancer treatment. While diet, probiotics, and faecal microbiota transplant are primary avenues of therapy focused on restoring or protecting gut function in people undergoing cancer treatment, the role of physical activity and exercise has scarcely been examined in this population.<br><br>METHODS: A narrative review was conducted to explore the nexus between cancer care and the gut microbiome in the context of physical activity and exercise as a widely available and clinically effective supportive care strategy used by cancer survivors.<br><br>RESULTS: Exercise can facilitate a more diverse gut microbiome and functional metabolome in humans; however, most physical activity and exercise studies have been conducted in healthy or athletic populations, primarily using aerobic exercise modalities. A scarcity of exercise and microbiome studies in cancer exists.<br><br>CONCLUSIONS: Exercise remains an attractive avenue to promote microbiome health in cancer survivors. Future research should elucidate the various influences of exercise modalities, intensities, frequencies, durations, and volumes to explore dose-response relationships between exercise and the gut microbiome among cancer survivors, as well as multifaceted approaches (such as diet and probiotics), and examine the influences of exercise on the gut microbiome and associated symptom burden prior to, during, and following cancer treatment.}, }
@article {pmid38012292, year = {2023}, author = {Wang, LJ and Jin, YL and Pei, WL and Li, JC and Zhang, RL and Wang, JJ and Lin, W}, title = {Amuc_1100 pretreatment alleviates acute pancreatitis in a mouse model through regulating gut microbiota and inhibiting inflammatory infiltration.}, journal = {Acta pharmacologica Sinica}, volume = {}, number = {}, pages = {}, pmid = {38012292}, issn = {1745-7254}, abstract = {Amuc_1100 is a membrane protein from Akkermansia muciniphila, which has been found to play a role in host immunological homeostasis in the gastrointestinal tract by activating TLR2 and TLR4. In this study we investigated the effects and underlying mechanisms of Amuc_1100 on acute pancreatitis (AP) induced in mice by intraperitoneal injection of caerulein and lipopolysaccharide (LPS). The mice were treated with the protein Amuc_1100 (3 μg, i.g.) for 20 days before caerulein injection. Cecal contents of the mice were collected for 16S rRNA sequencing. We found that pretreatment with Amuc_1100 significantly alleviated AP-associated pancreatic injury, reduced serum amylase and lipase. Amuc_1100 pretreatment significantly inhibited the expression of proinflammatory cytokines (TNF-α, IL-1β, IFN-γ and IL-6) in spleen and pancreas through inhibiting NF-κB signaling pathway. Moreover, Amuc_1100 pretreatment significantly decreased the inflammatory infiltration, accompanied by the reduction of Ly6C[+] macrophages and neutrophils in the spleen of AP mice. Gut microbiome analysis showed that the abundance of Bacteroidetes, Proteobacteria, Desulfobacterota and Campilobacterota was decreased, while the proportion of Firmicutes and Actinobacteriota was increased in AP mice pretreated with Amuc_1100. We further demonstrated that Amuc_1100 pretreatment restored the enrichment of tryptophan metabolism, which was mediated by intestinal flora. These results provide new evidence that Amuc_1100 lessens the severity of AP through its anti-inflammatory properties with a reduction of macrophages and neutrophil infiltration, as well as its regulation of the composition of intestinal flora and tryptophan metabolism.}, }
@article {pmid38012110, year = {2023}, author = {Zou, X and Nakura, Y and Kawaguchi, H and Nishiumi, F and Wu, HN and Yanagihara, I}, title = {Comparison of databases useful for the analysis of vaginal microbiota in Japanese women using next-generation sequencing data (QIIME 2 software).}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxad283}, pmid = {38012110}, issn = {1365-2672}, abstract = {AIMS: Approximately 10% of children are born prematurely, and bacterial vaginosis during pregnancy is associated with preterm delivery. Highly accurate species-level vaginal microflora analysis helps control bacteria-induced preterm birth. Therefore, we aimed to conduct a bioinformatic analysis of gene sequences using 16S databases and compare their efficacy in comprehensively identifying potentially pathogenic vaginal microbiota in Japanese women.<br><br>METHODS AND RESULTS: The 16s rRNA databases, Silva, Greengenes, and basic local alignment search tool (BLAST) were compared to determine whether the classification quality could be improved using the V3-V4 region next-generation sequencing (NGS) sequences. It was found that NGS data were aligned using the BLAST database with the QIIME 2 platform, whose classification quality was higher than that of Silva, and the combined Silva and Greengenes databases based on the mutual complementarity of the two databases.<br><br>CONCLUSIONS: The reference database selected during the bioinformatic processing influenced the recognized sequence percentage, taxonomic rankings, and accuracy. This study showed that the BLAST database was the best choice for NGS data analysis of Japanese women's vaginal microbiota.}, }
@article {pmid38011708, year = {2023}, author = {Moody, M and Sawyer, R}, title = {Is There a Community Microbial Community? A Comparison of Pathogens Between Two Hospital Surgical Intensive Care Units in a Single City.}, journal = {Surgical infections}, volume = {}, number = {}, pages = {}, doi = {10.1089/sur.2023.069}, pmid = {38011708}, issn = {1557-8674}, abstract = {Background: Nosocomial and health-care-associated infections drive increased healthcare costs and negatively affect patient outcomes. The human microbiome has been heavily explored in recent years with incomplete data regarding hospital-specific and community-specific microbial communities. Although bacterial species differ between intensive care units in the same hospital, it is unclear if they differ between similar units in similar hospitals in the same community. Our hypothesis is that pathogens in surgical intensive care units (SICUs) are distinct between hospitals, even in the same community. Methods: From 2017 to 2021, data were collected prospectively from the SICUs of two 400-bed hospitals located three miles apart in the same city (Hospital A and Hospital B). Infections defined using U.S. Centers for Disease Control and Prevention (CDC) criteria were recorded for trauma and general surgery patients, as well as patient demographics, Acute Physiology and Chronic Health Evaluation (APACHE) II score, and causative organism. Results: Overall, Escherichia coli was the most commonly isolated pathogen in Hospital A, whereas Staphylococcus aureus was most commonly isolated at Hospital B. Enterococci were more common in Hospital A, and Haemophilus influenzae and Enterobacter spp. were more common in Hospital B. After stratification between trauma and non-trauma patients, however, these differences disappeared, with the exception of more overall gram-positive organisms and fewer gram-negative organisms among Hospital A trauma patients compared to Hospital B. There were no differences in rates of isolation of either fungi or resistant bacteria between hospitals. Conclusions: At a species level, admission diagnosis appears to be a greater determinant of pathogen isolation than hospital when comparing similar intensive care units (ICUs) in the same geographic area, but a larger body of data is needed to flesh out a distinct microbial map of the organisms occupying a certain geographic region. Further areas for investigation include comparison between hospital units, specific anatomic sites, and ICU versus floor patients.}, }
@article {pmid38011635, year = {2023}, author = {Choueiry, F and Gold, A and Xu, R and Zhang, S and Zhu, J}, title = {Secondary-Electrospray Ionization Mass Spectrometry-Based Online Analyses of Mouse Volatilome Uncover Gut Microbiome-Dictated Metabolic Changes in the Host.}, journal = {Journal of the American Society for Mass Spectrometry}, volume = {}, number = {}, pages = {}, doi = {10.1021/jasms.3c00304}, pmid = {38011635}, issn = {1879-1123}, abstract = {The symbiotic relationship between the gut microbial population is capable of regulating numerous aspects of host physiology, including metabolism. Bacteria can modulate the metabolic processes of the host by feeding on nutritional components within the lumen and releasing bioactive components into circulation. Endogenous volatile organic compound (VOC) synthesis is dependent on the availability of precursors found in mammalian metabolism. Herein, we report that microbial-mediated metabolic influences can alter the host volatilome and the prominent volatile changes can be uncovered by a novel volatile analysis technique named secondary electrospray ionization mass spectrometry. Mice were subjected to an antibiotic cocktail to deplete the microbiome and then inoculated with either single strain bacteria or fecal matter transplantation (FMT) to replete the microbial population in the gut. VOC sampling was achieved by using an advanced secondary electrospray ionization (SESI) source that directly mounted onto a Thermo Q-Exactive high-resolution mass spectrometer (HRMS). A principal component analysis summarizing the volatile profiles of the mice revealed independent clustering of each strain of the FMT-inoculated groups, suggesting unique volatile profiles. The Mummichog algorithm uncovered phenylalanine metabolism as a significantly altered metabolic profile in the volatilome of the microbiome-repleted mice. Our results indicated that the systemic metabolic changes incurred by the host are translated to unique volatile profiles correlated to the diversity of the microbial population colonized within the host. It is thus possible to take advantage of SESI-HRMS-based platforms for noninvasive screening of VOCs to determine the contribution of various microbial colonization within human gut that may impact host health.}, }
@article {pmid38011171, year = {2023}, author = {Tomita, S and Kuroda, K and Narihiro, T}, title = {A small step to discover candidate biological control agents from preexisting bioresources by using novel nonribosomal peptide synthetases hidden in activated sludge metagenomes.}, journal = {PloS one}, volume = {18}, number = {11}, pages = {e0294843}, pmid = {38011171}, issn = {1932-6203}, abstract = {Biological control agents (BCAs), beneficial organisms that reduce the incidence or severity of plant disease, have been expected to be alternatives to replace chemical pesticides worldwide. To date, BCAs have been screened by culture-dependent methods from various environments. However, previously unknown BCA candidates may be buried and overlooked because this approach preferentially selects only easy-to-culture microbial lineages. To overcome this limitation, as a small-scale test case, we attempted to explore novel BCA candidates by employing the shotgun metagenomic information of the activated sludge (AS) microbiome, which is thought to contain unutilized biological resources. We first performed genome-resolved metagenomics for AS taken from a municipal sewage treatment plant and obtained 97 nonribosomal peptide synthetase (NRPS)/polyketide synthase (PKS)-related gene sequences from 43 metagenomic assembled bins, most of which were assigned to the phyla Proteobacteria and Myxococcota. Furthermore, these NRPS/PKS-related genes are predicted to be novel because they were genetically dissimilar to known NRPS/PKS gene clusters. Of these, the condensation domain of the syringomycin-related NRPS gene cluster was detected in Rhodoferax- and Rhodocyclaceae-related bins, and its homolog was found in previously reported AS metagenomes as well as the genomes of three strains available from the microbial culture collections, implying their potential BCA ability. Then, we tested the antimicrobial activity of these strains against phytopathogenic fungi to investigate the potential ability of BCA by in vitro cultivation and successfully confirmed the actual antifungal activity of three strains harboring a possibly novel NRPS gene cluster. Our findings provide a possible strategy for discovering novel BCAs buried in the environment using genome-resolved metagenomics.}, }
@article {pmid38011083, year = {2023}, author = {Chalifour, BN and Elder, LE and Li, J}, title = {Diversity of gut microbiome in Rocky Mountainsnail across its native range.}, journal = {PloS one}, volume = {18}, number = {11}, pages = {e0290292}, pmid = {38011083}, issn = {1932-6203}, abstract = {The animal gut microbiome is often a key requirement for host nutrition, digestion, and immunity, and can shift in relation to host geography and environmental factors. However, ecological drivers of microbiome community assembly across large geographic ranges have rarely been examined in invertebrates. Oreohelix strigosa (Rocky Mountainsnail) is a widespread land snail found in heterogeneous environments across the mountainous western United States. It is ideally suited for biogeography studies due to its broad distribution, low migration, and low likelihood of passive transport via other animals. This study aims to uncover large-scale geographic shifts in the composition of O. strigosa gut microbiomes by using 16S rRNA gene sequencing on samples from across its native range. Additionally, we elucidate smaller-scale microbiome variation using samples collected only within Colorado. Results show that gut microbiomes vary significantly across broad geographic ranges. Several possible ecological drivers, including soil and vegetation composition, habitat complexity, habitat type, and human impact, collectively explained 27% of the variation across Coloradan O. strigosa gut microbiomes. Snail gut microbiomes show more similarity to vegetation than soil microbiomes. Gut microbial richness was highest in the rocky habitats and increased significantly in the most disturbed habitats (low complexity, high human impact), potentially indicating signs of dysbiosis in the snails' gut microbiomes. These small-scale environmental factors may be driving changes in O. strigosa gut microbiome composition seen across large-scale geography. This knowledge will also help us better understand how microbial associations influence species survival in diverse environments and aid wildlife conservation efforts.}, }
@article {pmid38010921, year = {2023}, author = {Fenneman, AC and Boulund, U and Collard, D and Galenkamp, H and Zwinderman, A and van der Born, BJ and van der Spek, AH and Fliers, E and Rampanelli, E and Blaser, M and Nieuwdorp, M}, title = {Comparative Analysis of Taxonomic and Functional Gut Microbiota Profiles in Relation to Seroconversion of Thyroid Peroxidase Antibodies in Euthyroid Participants.}, journal = {Thyroid : official journal of the American Thyroid Association}, volume = {}, number = {}, pages = {}, doi = {10.1089/thy.2023.0346}, pmid = {38010921}, issn = {1557-9077}, abstract = {BACKGROUND: Previous studies have reported gut microbiome alterations in Hashimoto's autoimmune thyroiditis (HT) patients. Yet, it is unknown whether an aberrant microbiome is present before clinical disease onset in participants susceptible to HT or whether it reflects the effects of the disease itself. Here, we report for the first time a comprehensive characterization of the taxonomic and functional profiles of the gut microbiota in euthyroid seropositive and seronegative participants. Our primary goal was to determine taxonomic and functional signatures of the intestinal microbiota associated with serum thyroid peroxidase antibodies (TPOAb) antibodies. A secondary aim was to determine whether different ethnicities warrant distinct reference intervals for accurate interpretation of serum thyroid biomarkers.<br><br>METHODS: In this cross-sectional study, euthyroid participants with (N=159) and without (N=1,309) TPOAb were selected from the multi-ethnic (European Dutch, Moroccan, and Turkish) HEalthy Life In an Urban Setting (HELIUS) cohort. Fecal microbiota composition was profiled using 16S rRNA sequencing. Differences between the groups were analyzed based on overall composition (alpha and beta diversity), as well as differential abundance of microbial taxa and functional pathways using multiple differential abundance tools.<br><br>RESULTS: Overall composition showed a substantial overlap between the two groups (p>0.05 for alpha-diversity; p=0.39 for beta-diversity), indicating that TPOAb-seropositivity does not significantly differentiate gut microbiota composition and diversity. Interestingly, TPOAb-status accounted for only a minor fraction (0.07%) of microbiome variance (p=0.545). Further exploration of taxonomic differences identified 138 taxa nominally associated with TPOAb-status. Among these, thirteen taxa consistently demonstrated nominal significance across three additional differential abundance methods, alongside notable associations within various functional pathways. Furthermore, we showed that ethnicity-specific reference intervals for serum thyroid biomarkers are not required, as no significant disparities in serum thyroid markers were found among the three ethnic groups residing in an iodine-replete area (p>0.05 for TSH, fT4, and TPOAb).<br><br>CONCLUSION: These findings suggest that there is no robust difference in gut microbiome between individuals with or without TPOAb in terms of alpha and beta-diversity. Nonetheless, several taxa were identified with nominal significance related to TPOAb presence. Further research is required to determine whether these changes indeed imply a higher risk of overt HT.}, }
@article {pmid38010886, year = {2023}, author = {Garrett, S and Asada, MC and Sun, J}, title = {Axin1's mystique in manipulating microbiome amidst colitis.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2286674}, doi = {10.1080/19490976.2023.2286674}, pmid = {38010886}, issn = {1949-0984}, abstract = {Classically, Axin1 is considered a regulator of Wnt/β-catenin signaling. However, Axin1's roles in host-microbial interactions have been unknown. Our recent study has demonstrated that deletion of intestinal epithelial Axin1 in epithelial cells and Paneth cells protects the host against colitis by enhancing Akkermansia muciniphila. Loss of intestinal epithelial or Paneth cell Axin1 results in increased Wnt/β-catenin signaling, proliferation, and cell migration. This is associated with morphologically altered goblet and Paneth cells, including increased Muc2 and decreased lysozyme. Axin1 deletion specifically enriched Akkermansia muciniphila. Akkermansia muciniphila in Axin1 knockout mice is the driver of protection against DSS-induced inflammation. Here, we feature several significant conceptual changes, such as differences between Axin1 and Axin2, Axin1 in innate immunity and microbial homeostasis, and Axin1 reduction of Akkermansia muciniphila. We discuss an important trend in the field related to Paneth cells and tissue-specific Axin1 manipulation of microbiome in health and inflammation.}, }
@article {pmid38010871, year = {2023}, author = {Jinato, T and Sikaroodi, M and Fagan, A and Sterling, RK and Lee, H and Puri, P and Davis, BC and Fuchs, M and Gavis, E and Gillevet, PM and Bajaj, JS}, title = {Alterations in gut virome are associated with cognitive function and minimal hepatic encephalopathy cross-sectionally and longitudinally in cirrhosis.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2288168}, doi = {10.1080/19490976.2023.2288168}, pmid = {38010871}, issn = {1949-0984}, abstract = {Cognitive dysfunction due to minimal hepatic encephalopathy (MHE) adversely impacts patients with cirrhosis and more precise therapies are needed. Gut-brain axis changes are therapeutic targets, but prior studies have largely focused on bacterial changes. Our aim was to determine linkages between individual cognitive testing results and bacteria with the virome using a cross-sectional and longitudinal approach. We included cross-sectional (n = 138) and longitudinal analyses (n = 36) of patients with cirrhosis tested using three cognitive modalities, which were psychometric hepatic encephalopathy score (PHES), inhibitory control test (ICT), Stroop, and all three. Stool metagenomics with virome and bacteriome were analyzed studied cross-sectionally and in a subset followed for development/reversal of MHE repeated at 6 months (longitudinally only using PHES). Cross-sectional: We found no significant changes in α/β diversity in viruses or bacteria regardless of cognitive testing. Cognitively impaired patients were more likely to have higher relative abundance of bacteriophages linked with Streptococcus, Faecalibacterium, and Lactobacillus, which were distinct based on modality. These were also linked with cognition on correlation networks. Longitudinally, 27 patients remained stable while 9 changed their MHE status. Similar changes in phages that are linked with Streptococcus, Faecalibacterium, and Lactobacillus were seen. These phages can influence ammonia, lactate, and short-chain fatty acid generation, which are neuro-active. In conclusion, we found linkages between bacteriophages and cognitive function likely due to impact on bacteria that produce neuroactive metabolites cross-sectionally and longitudinally. These findings could help explore bacteriophages as options to influence treatment for MHE in cirrhosis.}, }
@article {pmid38010793, year = {2023}, author = {Li, H and Liu, C and Huang, S and Wang, X and Cao, M and Gu, T and Ou, X and Pan, S and Lin, Z and Wang, X and Zhu, Y and Jing, J}, title = {Multi-omics analyses demonstrate the modulating role of gut microbiota on the associations of unbalanced dietary intake with gastrointestinal symptoms in children with autism spectrum disorder.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2281350}, doi = {10.1080/19490976.2023.2281350}, pmid = {38010793}, issn = {1949-0984}, abstract = {Our previous work revealed that unbalanced dietary intake was an important independent factor associated with constipation and gastrointestinal (GI) symptoms in children with autism spectrum disorder (ASD). Growing evidence has shown the alterations in the gut microbiota and gut microbiota-derived metabolites in ASD. However, how the altered microbiota might affect the associations between unbalanced diets and GI symptoms in ASD remains unknown. We analyzed microbiome and metabolomics data in 90 ASD and 90 typically developing (TD) children based on 16S rRNA and untargeted metabolomics, together with dietary intake and GI symptoms assessment. We found that there existed 11 altered gut microbiota (FDR-corrected P-value <0.05) and 397 altered metabolites (P-value <0.05) in children with ASD compared with TD children. Among the 11 altered microbiota, the Turicibacter, Coprococcus 1, and Lachnospiraceae FCS020 group were positively correlated with constipation (FDR-corrected P-value <0.25). The Eggerthellaceae was positively correlated with total GI symptoms (FDR-corrected P-value <0.25). More importantly, three increased microbiota including Turicibacter, Coprococcus 1, and Eggerthellaceae positively modulated the associations of unbalanced dietary intake with constipation and total GI symptoms, and the decreased Clostridium sp. BR31 negatively modulated their associations in ASD children (P-value <0.05). Together, the altered microbiota strengthens the relationship between unbalanced dietary intake and GI symptoms. Among the altered metabolites, ten metabolites derived from microbiota (Turicibacter, Coprococcus 1, Eggerthellaceae, and Clostridium sp. BR31) were screened out, enriched in eight metabolic pathways, and were identified to correlate with constipation and total GI symptoms in ASD children (FDR-corrected P-value <0.25). These metabolomics findings further support the modulating role of gut microbiota on the associations of unbalanced dietary intake with GI symptoms. Collectively, our research provides insights into the relationship between diet, the gut microbiota, and GI symptoms in children with ASD.}, }
@article {pmid38010636, year = {2023}, author = {Gladyshev, NS and Baram, DV and Gorbunova, AV and Krivolapov, YA}, title = {[Transcriptome analysis of tissue microbiota diversity in tumor and non-tumor lymph nodes].}, journal = {Arkhiv patologii}, volume = {85}, number = {6}, pages = {26-30}, doi = {10.17116/patol20238506126}, pmid = {38010636}, issn = {0004-1955}, abstract = {BACKGROUND: Metagenomic studies in recent years have demonstrated that all tissues of the human body studied by genomic and transcriptomic sequencing methods, both in pathological processes and in normality, contain fragments of DNA and RNA from a variety of microorganisms. The composition of tissue microbiota and its relationship with development of pathological changes are still poorly understood, despite increasing number of studies in this area every year. In this study, gene expression of the lymph node microbiome in reactive follicular hyperplasia and follicular lymphoma was investigated.<br><br>OBJECTIVE: To study expression of lymph node microbiome genes in reactive follicular hyperplasia and follicular lymphoma.<br><br>MATERIAL AND METHODS: The work included 38 biopsy samples of lymph nodes with follicular lymphoma of different cytological subtypes and 10 biopsy samples of lymph nodes with reactive follicular hyperplasia. Verification of diagnosis was carried out using standard histological, histochemical and immunohistochemical methods. Using sequencing method, the transcriptome was examined. Statistical analysis and data visualization were performed using the R programming language (version 4.2.1).<br><br>RESULTS: Tumor lymph nodes are characterized by large Simpson and Shannon alpha diversity values (p-value = 0.026465 and p-value = 0.007122, respectively). Two clusters were discovered, characterized by different levels of relative abundance of microorganisms.<br><br>CONCLUSION: It has been proven that diversity of microorganisms present in tumor tissue and their number are statistically significantly higher than corresponding indicators in the lymph nodes with follicular hyperplasia.}, }
@article {pmid38010368, year = {2023}, author = {Yeo, XY and Chae, WR and Lee, HU and Bae, HG and Pettersson, S and Grandjean, J and Han, W and Jung, S}, title = {Nuanced contribution of gut microbiome in the early brain development of mice.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2283911}, doi = {10.1080/19490976.2023.2283911}, pmid = {38010368}, issn = {1949-0984}, abstract = {The complex symbiotic relationship between the mammalian body and gut microbiome plays a critical role in the health outcomes of offspring later in life. The gut microbiome modulates virtually all physiological functions through direct or indirect interactions to maintain physiological homeostasis. Previous studies indicate a link between maternal/early-life gut microbiome, brain development, and behavioral outcomes relating to social cognition. Here we present direct evidence of the role of the gut microbiome in brain development. Through magnetic resonance imaging (MRI), we investigated the impact of the gut microbiome on brain organization and structure using germ-free (GF) mice and conventionalized mice, with the gut microbiome reintroduced after weaning. We found broad changes in brain volume in GF mice that persist despite the reintroduction of gut microbes at weaning. These data suggest a direct link between the maternal gut or early-postnatal microbe and their impact on brain developmental programming.}, }
@article {pmid38010361, year = {2023}, author = {Nori, SRC and McGuire, TK and Lawton, EM and McAuliffe, FM and Sinderen, DV and Walsh, CJ and Cotter, PD and Feehily, C}, title = {Profiling of vaginal Lactobacillus jensenii isolated from preterm and full-term pregnancies reveals strain-specific factors relating to host interaction.}, journal = {Microbial genomics}, volume = {9}, number = {11}, pages = {}, doi = {10.1099/mgen.0.001137}, pmid = {38010361}, issn = {2057-5858}, abstract = {Each year, 15 million infants are born preterm (<37 weeks gestation), representing the leading cause of mortality for children under the age of five. Whilst there is no single cause, factors such as maternal genetics, environmental interactions, and the vaginal microbiome have been associated with an increased risk of preterm birth. Previous studies show that a vaginal microbiota dominated by Lactobacillus is, in contrast to communities containing a mixture of genera, associated with full-term birth. However, this binary principle does not fully consider more nuanced interactions between bacterial strains and the host. Here, through a combination of analyses involving genome-sequenced isolates and strain-resolved metagenomics, we identify that L. jensenii strains from preterm pregnancies are phylogenetically distinct from strains from full-term pregnancies. Detailed analysis reveals several genetic signatures that distinguish preterm birth strains, including genes predicted to be involved in cell wall synthesis, and lactate and acetate metabolism. Notably, we identify a distinct gene cluster involved in cell surface protein synthesis in our preterm strains, and profiling the prevalence of this gene cluster in publicly available genomes revealed it to be predominantly present in the preterm-associated clade. This study contributes to the ongoing search for molecular biomarkers linked to preterm birth and opens up new avenues for exploring strain-level variations and mechanisms that may contribute to preterm birth.}, }
@article {pmid38010168, year = {2023}, author = {Ye, H and Ghosh, TS and Hueston, CM and Vlckova, K and Golubeva, AV and Hyland, NP and O'Toole, PW}, title = {Engraftment of aging-related human gut microbiota and the effect of a seven-species consortium in a pre-clinical model.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2282796}, doi = {10.1080/19490976.2023.2282796}, pmid = {38010168}, issn = {1949-0984}, abstract = {Human aging is characterized by gut microbiome alteration and differential loss of gut commensal species associated with the onset of frailty. The administration of cultured commensal strains to replenish lost taxa could potentially promote healthy aging. To investigate the interaction of whole microbiomes and administered strains, we transplanted gut microbiota from a frail or healthy elderly subject into germ-free mice. We supplemented the frail-donor recipient group with a defined consortium of taxa (the "S7") that we identified by analyzing healthy aging subjects in our previous studies and whose abundance correlated with health-promoting dietary intervention. Inoculation with a frail or a healthy donor microbiome resulted in differential microbiota compositions in murine recipients 5 weeks post-transplantation. Fecal acetate levels were significantly higher in healthy donor recipient mice than in frail donor recipient mice after 4 weeks. However, the frailty-related phenotype was not replicated in recipient mice with single-dose microbiota transplantation from a healthy and a frail donor. Five S7 species colonized successfully in germ-free mice, with a relatively high abundance of Barnesiella intestinihominis and Eubacterium rectale. The engraftment of five S7 species in germ-free mice increased fecal acetate levels and reduced colon permeability and plasma TNF-ɑ concentration. Supplementation with the S7 in frail-microbiota recipient mice did not increase alpha-diversity but significantly increased the abundance of Barnesiella intestinihominis. S7 supplementation showed the potential for improving spatial reference memory in frail-microbiota recipient mice. Collectively, these data highlight the challenge of elderly microbiota engraftment in the germ-free mouse model but show promise for modulating the gut microbiome of frail elderly subjects by administering an artificial gut microbe consortium associated with healthy aging.}, }
@article {pmid38010080, year = {2023}, author = {Luoto, R and Pärtty, A and Vogt, JK and Rautava, S and Isolauri, E}, title = {Reversible aberrancies in gut microbiome of moderate and late preterm infants: results from a randomized, controlled trial.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2283913}, doi = {10.1080/19490976.2023.2283913}, pmid = {38010080}, issn = {1949-0984}, abstract = {The aim of this study was to obtain insight into the composition and function of the deviant gut microbiome throughout infancy in children born moderately and late preterm and their response to microbiome modulation. We characterized the longitudinal development of the gut microbiome from birth to the age of 12 months by metagenomic sequencing in 43 moderate and late preterm children participating in a randomized, controlled trial (ClinicalTrials.gov/no.NCT00167700) assessing the impact of a probiotic (Lactobacillus rhamnosus GG, ATCC 53,103, currently Lacticaseibacillus rhamnosus GG) and a prebiotic (galacto-oligosaccharide and polydextrose mixture, 1:1) intervention as compared to a placebo administered from 3 to 60 days of life. In addition, 9 full-term, vaginally delivered, breast-fed infants, who remained healthy long-term were included as references. Significant differences in taxonomy, but not in functional potential, were found when comparing the gut microbiome composition of preterm and full-term infants during the first month of life. However, the gut microbiome of preterm infants resembled that of full-term infants by 6 months age. Probiotic and prebiotic treatments were found to mitigate the shift in the microbiome of preterm infants by accelerating Bifidobacteria-dominated gut microbiome in beta diversity analysis. This study provides intriguing information regarding the establishment of the gut microbiome in children born moderately and late preterm, representing the majority of children born preterm. Specific pro- and prebiotics may reverse the proinflammatory gut microbiome composition during the vulnerable period, when the microbiome is low in resilience and susceptible to environmental exposure and simultaneously promotes immunological and metabolic maturation.}, }
@article {pmid38010059, year = {2023}, author = {Zhong, J and Xiong, D and Liu, Y and Yuan, S}, title = {Association of antibiotic exposure with survival in patients with extensive-stage small cell lung cancer receiving immune checkpoint inhibitor therapy.}, journal = {Thoracic cancer}, volume = {}, number = {}, pages = {}, doi = {10.1111/1759-7714.15172}, pmid = {38010059}, issn = {1759-7714}, support = {NSFC82073345//National Natural Science Foundation of China/ ; //Taishan Scholars Program to Shuanghu Yuan/ ; 202019060//Jinan Clinical Medicine Science and Technology Innovation Plan/ ; ZR202209010002//Natural Science Innovation and Development Joint Foundation of Shandong Province/ ; }, abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) have dramatically shifted the therapeutic paradigm of extensive-stage small cell lung cancer (ES-SCLC). Antibiotic (ATB) exposure before or during ICI therapy can harm the integrity of the gut microbiome and lead to intestinal dysbiosis, which has a profoundly negative impact on the treatment response for various malignancies. Whether this is applicable to ES-SCLC remains unclear.<br><br>METHODS: We retrospectively reviewed the electronic medical records of all patients diagnosed with ES-SCLC who were treated with ICI-based immunotherapies from July 2019 to December 2020 at Shandong Cancer Hospital and Institute, China. Outcomes with the use of ATBs before or after the first infusion of ICI, including progression-free survival (PFS) and overall survival (OS), were investigated using the Kaplan-Meier method. Multivariate analyses were also conducted using a Cox proportional hazards model.<br><br>RESULTS: A total of 214 patients were included, among whom 41 (19.2%) received ATBs within 2&#x2009;months before or after the first initiation of ICI therapy and were assigned to the ATB group. The ATB group showed a shorter median PFS (4.3 vs. 6.3&#x2009;months; HR&#x2009;=&#x2009;1.43, 95% CI: 0.97-2.11; p&#x2009;=&#x2009;0.043) and a significantly shorter median OS (6.9 vs. 13&#x2009;months; HR&#x2009;=&#x2009;1.47, 95% CI: 0.98-2.20; p&#x2009;=&#x2009;0.033) than the non-ATB group. In the multivariate analysis, ATB exposure was markedly associated with worse PFS (HR&#x2009;=&#x2009;1.47, 95% CI: 1.03-2.09, p&#x2009;=&#x2009;0.035) and OS (HR&#x2009;=&#x2009;1.46, 95% CI: 1.01-2.11, p&#x2009;=&#x2009;0.043).<br><br>CONCLUSIONS: Our results demonstrate that ATB exposure was significantly associated with worse survival in ES-SCLC patients who received ICI therapy.}, }
@article {pmid38009922, year = {2023}, author = {Tsitouras, A and Al-Ghussain, N and Butcher, J and Stintzi, A and Delatolla, R}, title = {The microbiome of two strategies for ammonia removal with the sequencing batch moving bed biofilm reactor treating cheese production wastewater.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0150723}, doi = {10.1128/aem.01507-23}, pmid = {38009922}, issn = {1098-5336}, abstract = {Cheese production facilities must abide by sewage discharge bylaws that prevent overloading municipal water resource recovery facilities, eutrophication, and toxicity to aquatic life. Compact treatment systems can permit on-site treatment of cheese production wastewater; however, competition between heterotrophs and nitrifiers impedes the implementation of the sequencing batch moving bed biofilm reactor (SB-MBBR) for nitrification from high-carbon wastewaters. This study demonstrates that a single SB-MBBR is not feasible for nitrification when operated with anerobic and aerobic cycling for carbon and phosphorous removal from cheese production wastewater, as nitrification does not occur in a single reactor. Thus, two reactors in series are recommended to achieve nitrification from cheese production wastewater in SB-MBBRs. These findings can be applied to pilot and full-scale SB-MBBR operations. By demonstrating the potential to implement partial nitrification in the SB-MBBR system, this study presents the possibility of implementing partial nitrification in the SB-MBBR, resulting in the potential for more sustainable treatment of nitrogen from cheese production wastewater.}, }
@article {pmid38009901, year = {2023}, author = {Szaleniec, J and Bezshapkin, V and Krawczyk, A and Kopera, K and Zapała, B and Gosiewski, T and Kosciolek, T}, title = {Determinants of the microbiome spatial variability in chronic rhinosinusitis.}, journal = {Rhinology}, volume = {}, number = {}, pages = {}, doi = {10.4193/Rhin22.423}, pmid = {38009901}, issn = {0300-0729}, abstract = {BACKGROUND: The sinus microbiome in patients with chronic rhinosinusitis (CRS) is considered homogenous across the sinonasal cavity. The middle nasal meatus is the recommended sampling site for 16S rRNA sequencing. However, individuals with unusually high between-site variability between the middle meatus and the sinuses were identified in previous studies. This study aimed to identify which factors determine increased microbial heterogeneity between sampling sites in the sinuses.<br><br>METHODOLOGY: In this cross-sectional study samples for 16S rRNA sequencing were obtained from the middle meatus, the maxillary and the frontal sinus in 50 patients with CRS. The microbiome diversity between sampling sites was analysed in relation to the size of the sinus ostia and clinical metadata.<br><br>RESULTS: In approximately 15% of study participants, the differences between sampling sites within one patient were greater than between the patient and other individuals. Contrary to a popular hypothesis, obstruction of the sinus ostium resulted in decreased dissimilarity between the sinus and the middle meatus. The dissimilarity between the sampling sites was patient-specific: greater between-sinus differences were associated with greater meatus-sinus differences, regardless of the drainage pathway patency. Decreased spatial variability was observed in patients with nasal polyps and extensive mucosal changes in the sinuses.<br><br>CONCLUSIONS: Sampling from the middle meatus is not universally representative of the sinus microbiome. The differences between sites cannot be predicted from the patency of communication pathways between them.}, }
@article {pmid38009763, year = {2023}, author = {Szymanski, EA and Turner, M}, title = {Metaphors as design tools for microbial consortia: An analysis of recent peer-reviewed literature.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.14366}, pmid = {38009763}, issn = {1751-7915}, support = {2042475//Division of Social and Economic Sciences/ ; }, abstract = {Single engineered microbial species cannot always conduct complex transformations, while complex, incompletely defined microbial consortia have heretofore been suited to a limited range of tasks. As biodesigners bridge this gap with intentionally designed microbial communities, they will, intentionally or otherwise, build communities that embody particular ideas about what microbial communities can and should be. Here, we suggest that metaphors-ideas about what microbial communities are like-are therefore important tools for designing synthetic consortia-based bioreactors. We identify a range of metaphors currently employed in peer-reviewed microbiome research articles, characterizing each through its potential structural implications and distinctive imagery. We present this metaphor catalogue in the interest of, first, making metaphors visible as design choices, second, enabling deliberate experimentation with them towards expanding the potential design space of the field, and third, encouraging reflection on the goals and values they embed.}, }
@article {pmid38009697, year = {2023}, author = {Molina, MA and Melchers, WJG}, title = {Methodological and analytical challenges in microbiome-HPV association studies.}, journal = {Journal of medical virology}, volume = {95}, number = {11}, pages = {e29260}, doi = {10.1002/jmv.29260}, pmid = {38009697}, issn = {1096-9071}, }
@article {pmid38009508, year = {2023}, author = {Cameron, O and Neves, JF and Gentleman, E}, title = {Listen to Your Gut: Key Concepts for Bioengineering Advanced Models of the Intestine.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2302165}, doi = {10.1002/advs.202302165}, pmid = {38009508}, issn = {2198-3844}, support = {MR/X008789/1/MRC_/Medical Research Council/United Kingdom ; NC/X002497/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; NC/X002497/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; }, abstract = {The intestine performs functions central to human health by breaking down food and absorbing nutrients while maintaining a selective barrier against the intestinal microbiome. Key to this barrier function are the combined efforts of lumen-lining specialized intestinal epithelial cells, and the supportive underlying immune cell-rich stromal tissue. The discovery that the intestinal epithelium can be reproduced in vitro as intestinal organoids introduced a new way to understand intestinal development, homeostasis, and disease. However, organoids reflect the intestinal epithelium in isolation whereas the underlying tissue also contains myriad cell types and impressive chemical and structural complexity. This review dissects the cellular and matrix components of the intestine and discusses strategies to replicate them in vitro using principles drawing from bottom-up biological self-organization and top-down bioengineering. It also covers the cellular, biochemical and biophysical features of the intestinal microenvironment and how these can be replicated in vitro by combining strategies from organoid biology with materials science. Particularly accessible chemistries that mimic the native extracellular matrix are discussed, and bioengineering approaches that aim to overcome limitations in modelling the intestine are critically evaluated. Finally, the review considers how further advances may extend the applications of intestinal models and their suitability for clinical therapies.}, }
@article {pmid38009223, year = {2023}, author = {Yu, J and Youngson, NA and Laybutt, DR and Morris, MJ and Leigh, SJ}, title = {Complementary yet divergent effects of exercise and an exercise mimetic on microbiome in high-fat diet-induced obesity.}, journal = {Physiological genomics}, volume = {}, number = {}, pages = {}, doi = {10.1152/physiolgenomics.00066.2023}, pmid = {38009223}, issn = {1531-2267}, support = {//Rebecca Cooper Foundation Grant/ ; //DHAC | National Health and Medical Research Council (NHMRC)/ ; //Department of Education and Training | Australian Research Council (ARC)/ ; //Australian Government Research Training Program/ ; //Australian Government Research Training Program/ ; }, abstract = {Exercise is beneficial for obesity, partially through increased mitochondrial activity and raised nicotinamide adenine dinucleotide, a coenzyme critical for mitochondrial function and metabolism. Recent work has shown that increasing the availability of nicotinamide adenine dinucleotide through pharmacological means improves metabolic health in rodent models of diet induced obesity, and that the effect of these supplements when administered orally may be modulated by the gut microbiome. The gut microbiome is altered by both diet and exercise, and is thought to contribute to some aspects of high-fat diet-induced metabolic dysfunction. We examined the independent and combined effects of treadmill exercise and nicotinamide mononucleotide (NMN) supplementation on the gut microbiome of female C57Bl6/J mice chronically fed a high-fat diet. We showed that 8 weeks of treadmill exercise, oral-administered NMN or combined therapy exert unique effects on gut microbiome composition without changing bacterial species richness. Exercise and NMN exerted additive effects on microbiota composition, and NMN partially or fully restored predicted microbial functions, specifically carbohydrate and lipid metabolism, to control levels. Further research is warranted to better understand the mechanisms underpinning the interactions between exercise and oral NAD[+] precursor supplementation on gut microbiome.}, }
@article {pmid38009162, year = {2023}, author = {Farooqi, MS and Podury, S and Crowley, G and Javed, U and Li, Y and Liu, M and Kwon, S and Grunig, G and Khan, AR and Francois, F and Nolan, A}, title = {Noninvasive, MultiOmic, and Multicompartmental Biomarkers of Reflux Disease: A Systematic Review.}, journal = {Gastro hep advances}, volume = {2}, number = {4}, pages = {608-620}, pmid = {38009162}, issn = {2772-5723}, support = {R01 HL119326/HL/NHLBI NIH HHS/United States ; U01 OH011300/OH/NIOSH CDC HHS/United States ; U01 OH011855/OH/NIOSH CDC HHS/United States ; U01 OH012069/OH/NIOSH CDC HHS/United States ; }, abstract = {BACKGROUND AND AIMS: Gastroesophageal reflux disease (GERD) is a prevalent gastrointestinal disorder that may complicate conditions such as obstructive airway disease. Our group has identified predictive biomarkers of GERD in particulate exposed first responders with obstructive airway disease. In addition, GERD diagnosis and treatment is costly and invasive. In light of these clinical concerns, we aimed to systematically review studies identifying noninvasive, multiOmic, and multicompartmental biomarkers of GERD.<br><br>METHODS: A systematic review of PubMed and Embase was performed using keywords focusing on reflux disease and biomarkers and registered with PROSPERO. We included original human studies in English, articles focusing on noninvasive biomarkers of GERD published after December 31, 2009. GERD subtypes (non-erosive reflux disease and erosive esophagitis) and related conditions (Barrett's Esophagus [BE] and Esophageal Adenocarcinoma). Predictive measures were synthesized and risk of bias assessed (Newcastle-Ottawa Scale).<br><br>RESULTS: Initial search identified n = 238 studies andn 13 articles remained after applying inclusion/exclusion criteria. Salivary pepsin was the most studied biomarker with significant sensitivity and specificity for GERD. Serum assessment showed elevated levels of Tumor Necrosis Factor-alpha in both GERD and Barrett's. Exhaled breath volatile sulfur compounds and acetic acid were associated with GERD. Oral Microbiome: Models with Lautropia, Streptococcus, and Bacteroidetes showed the greatest discrimination between BE and controls vs Lautropia; ROCAUC 0.94 (95% confidence interval; 0.85-1.00).<br><br>CONCLUSION: Prior studies identified significant multiOmic, multicompartmental noninvasive biomarker risks for GERD and BE. However, studies have a high risk of bias and the reliability and accuracy of the biomarkers identified are greatly limited, which further highlights the need to discover and validate clinically relevant noninvasive biomarkers of GERD.}, }
@article {pmid38009054, year = {2023}, author = {Zahra, A and Menon, R and Bento, GFC and Selim, J and Taylor, BD and Vincent, KL and Pyles, RB and Richardson, LS}, title = {Validation of vaginal microbiome proxies for in vitro experiments that biomimic Lactobacillus-dominant vaginal cultures.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {90}, number = {6}, pages = {e13797}, doi = {10.1111/aji.13797}, pmid = {38009054}, issn = {1600-0897}, support = {K12HD052023//NIH/NICHD/ ; //Building Interdisciplinary Research Careers in Women's Health Program-BIRCWH; Berenson, PI/ ; //National Institutes of Health/Office of the Director (OD)/National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01HD100729-01S1//Eunice Kennedy Shriver National Institute of Child Health &amp; Human Development (NICHD)/ ; //Institute for Translational Sciences/ ; UL1&#xa0;TR001439//Clinical and Translational Science/ ; //National Center for Advancing Translational Sciences at the National Institutes of Health (NIH)/ ; }, mesh = {Female ; Humans ; Lactobacillus/physiology ; Tumor Necrosis Factor-alpha/metabolism ; Interleukin-6/metabolism ; Interleukin-8/metabolism ; Vagina/microbiology ; *Vaginosis, Bacterial/microbiology ; Bacteria ; Anti-Inflammatory Agents ; *Microbiota ; }, abstract = {The vaginal microbiome includes diverse microbiota dominated by Lactobacillus [L.] spp. that protect against infections, modulate inflammation, and regulate vaginal homeostasis. Because it is challenging to incorporate vaginal microbiota into in vitro models, including organ-on-a-chip systems, we assessed microbial metabolites as reliable proxies in addition to traditional vaginal epithelial cultures (VECs). Human immortalized VECs cultured on transwells with an air-liquid interface generated stratified cell layers colonized by transplanted healthy microbiomes (L. jensenii- or L. crispatus-dominant) or a community representing bacterial vaginosis (BV). After 48-h, a qPCR array confirmed the expected donor community profiles. Pooled apical and basal supernatants were subjected to metabolomic analysis (untargeted mass spectrometry) followed by ingenuity pathways analysis (IPA). To determine the bacterial metabolites' ability to recreate the vaginal microenvironment in vitro, pooled bacteria-free metabolites were added to traditional VEC cultures. Cell morphology, viability, and cytokine production were assessed. IPA analysis of metabolites from colonized samples contained fatty acids, nucleic acids, and sugar acids that were associated with signaling networks that contribute to secondary metabolism, anti-fungal, and anti-inflammatory functions indicative of a healthy vaginal microbiome compared to sterile VEC transwell metabolites. Pooled metabolites did not affect cell morphology or induce cell death (∼5.5%) of VEC cultures (n = 3) after 72-h. However, metabolites created an anti-inflammatory milieu by increasing IL-10 production (p = .06, T-test) and significantly suppressing pro-inflammatory IL-6 (p = .0001), IL-8 (p = .009), and TNFα (p = .0007) compared to naïve VEC cultures. BV VEC conditioned-medium did not affect cell morphology nor viability; however, it induced a pro-inflammatory environment by elevating levels of IL-6 (p = .023), IL-8 (p = .031), and TNFα (p = .021) when compared to L.-dominate microbiome-conditioned medium. VEC transwells provide a suitable ex vivo system to support the production of bacterial metabolites consistent with the vaginal milieu allowing subsequent in vitro studies with enhanced accuracy and utility.}, }
@article {pmid38008735, year = {2023}, author = {Xiao, X and Cui, Y and Lu, H and Wang, J and Yang, J and Liu, L and Liu, Z and Peng, X and Cao, H and Liu, X and Wei, X}, title = {Strontium ranelate enriched Ruminococcus albus in the gut microbiome of Sprague-Dawley rats with postmenopausal osteoporosis.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {365}, pmid = {38008735}, issn = {1471-2180}, support = {2018QDJZR12//Cultivating Project for Young Scholar at Hubei University of Medicine/ ; 2015QDJZR06//Cultivating Project for Young Scholar at Hubei University of Medicine/ ; JC2022002//Innovation Research Program for Graduates of Basic Medical College, Hubei University of Medicine/ ; AD18281029//Guangxi Natural Science Foundation/ ; WJ2021M052//Hubei Provincial Health and Health Commission Funded Projects/ ; WJ2019Q025//Hubei Provincial Health and Health Commission Funded Projects/ ; }, mesh = {Humans ; Female ; Rats ; Animals ; Rats, Sprague-Dawley ; *Osteoporosis, Postmenopausal/drug therapy/metabolism ; *Gastrointestinal Microbiome ; Ruminococcus ; Lycopene/therapeutic use ; RNA, Ribosomal, 16S/genetics ; *Osteoporosis/drug therapy/metabolism ; }, abstract = {BACKGROUND: Gut microbiome is critical to our human health and is related to postmenopausal osteoporosis (PMO). Strontium ranelate (SrR) is an anti-osteoporosis oral drug that can promote osteoblast formation and inhibit osteoclast formation. However, the effect of SrR on gut microbiome has been rarely studied. Therefore, we investigated the effect of oral SrR on gut microbiome and metabolic profiles.<br><br>RESULTS: In this study, we used ovariectomized (OVX) Sprague-Dawley rats to construct a PMO model and applied oral SrR for 6 weeks. The relative abundance of intestinal microbiome was investigated by 16S rRNA metagenomic sequencing. Ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) was used to analyze changes in metabolites of intestinal contents. Results demonstrated that 6-week oral SrR alleviated osteoporosis and significantly changed the composition of the gut microbiome and metabolic profiles of OVX rats. Ruminococcus, Akkermansia and Oscillospira were significantly enriched in the gut of OVX rats after 6-week oral SrR. Especially, the species R. albus showed the greatest importance by a random forest classifier between OVX and OVX_Sr group. The enrichment of R. albus in the gut was positively correlated with bone mineral density and the accumulation of lycopene and glutaric acid, which also significantly elevated after oral SrR.<br><br>CONCLUSIONS: We discovered that oral SrR can improve bone health while stimulate the accumulation of gut microbe R. albus and metabolites (lycopene and glutaric acid). The results suggested possible connections between oral SrR and the gut-bone axis, which may provide new insight into the treatment/prevention of osteoporosis.}, }
@article {pmid38008696, year = {2023}, author = {Foppa, C and Rizkala, T and Repici, A and Hassan, C and Spinelli, A}, title = {Microbiota and IBD: Current knowledge and future perspectives.}, journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.dld.2023.11.015}, pmid = {38008696}, issn = {1878-3562}, abstract = {Inflammatory Bowel Disease (IBD) is a chronic relapsing-remitting disease with a remarkable increase in incidence worldwide and a substantial disease burden. Although the pathophysiology is not fully elucidated yet an aberrant immune reaction against the intestinal microbiota and the gut microbial dysbiosis have been identified to play a major role. The composition of gut microbiota in IBD patients is distinct from that of healthy individuals, with certain organisms predominating over others. Differences in the microbial dysbiosis have been also observed between Crohn Disease (CD) and Ulcerative Colitis (UC). A disruption of the microbiota's balance can lead to inflammation and intestinal damage. Microbiota composition in IBD can be affected both by endogenous (i.e., interaction with the immune system and intestinal epithelial cells) and exogenous (i.e., medications, surgery, diet) factors. The complex interplay between the gut microbiota and IBD is an area of great interest for understanding disease pathogenesis and developing new treatments. The purpose of this review is to summarize the latest evidence on the role of microbiota in IBD pathogenesis and to explore possible future areas of research.}, }
@article {pmid38008300, year = {2023}, author = {Gakis, G and Angelopoulos, I and Panagoulias, I and Mouzaki, A}, title = {Current knowledge on multiple sclerosis pathophysiology, disability progression assessment and treatment options, and the role of autologous hematopoietic stem cell transplantation.}, journal = {Autoimmunity reviews}, volume = {}, number = {}, pages = {103480}, doi = {10.1016/j.autrev.2023.103480}, pmid = {38008300}, issn = {1873-0183}, abstract = {Multiple sclerosis (MS) is an autoimmune disease of the central nervous system (CNS) that affects nearly 2.8 million people each year. MS distinguishes three main types: relapsing-remitting MS (RRMS), secondary progressive MS (SPMS) and primary progressive MS (PPMS). RRMS is the most common type, with the majority of patients eventually progressing to SPMS, in which neurological development is constant, whereas PPMS is characterized by a progressive course from disease onset. New or additional insights into the role of effector and regulatory cells of the immune and CNS systems, Epstein-Barr virus (EBV) infection, and the microbiome in the pathophysiology of MS have emerged, which may lead to the development of more targeted therapies that can halt or reverse neurodegeneration. Depending on the type and severity of the disease, various disease-modifying therapies (DMTs) are currently used for RRMS/SPMS and PPMS. As a last resort, and especially in highly active RRMS that does not respond to DMTs, autologous hematopoietic stem cell transplantation (AHSCT) is performed and has shown good results in reducing neuroinflammation. Nevertheless, the question of its potential role in preventing disability progression remains open. The aim of this review is to provide a comprehensive update on MS pathophysiology, assessment of MS disability progression and current treatments, and to examine the potential role of AHSCT in preventing disability progression.}, }
@article {pmid38007891, year = {2023}, author = {Solanki, MK and Joshi, NC and Singh, PK and Singh, SK and Santoyo, G and Basilio de Azevedo, LC and Kumar, A}, title = {From concept to reality: Transforming agriculture through innovative rhizosphere engineering for plant health and productivity.}, journal = {Microbiological research}, volume = {279}, number = {}, pages = {127553}, doi = {10.1016/j.micres.2023.127553}, pmid = {38007891}, issn = {1618-0623}, abstract = {The plant rhizosphere is regarded as a microbial hotspot due to a wide array of root exudates. These root exudates comprise diverse organic compounds such as phenolic, polysaccharides, flavonoids, fatty acids, and amino acids that showed chemotactic responses towards microbial communities and mediate significant roles in root colonization. The rhizospheric microbiome is a crucial driver of plant growth and productivity, contributing directly or indirectly by facilitating nutrient acquisition, phytohormone modulation, and phosphate solubilization under normal and stressful conditions. Moreover, these microbial candidates protect plants from pathogen invasion by secreting antimicrobial and volatile organic compounds. To enhance plant fitness and yield, rhizospheric microbes are frequently employed as microbial inoculants. However, recent developments have shifted towards targeted rhizosphere engineering or microbial recruitments as a practical approach to constructing desired plant rhizospheres for specific outcomes. The rhizosphere, composed of plants, microbes, and soil, can be modified in several ways to improve inoculant efficiency. Rhizosphere engineering is achieved through three essential mechanisms: a) plant-mediated modifications involving genetic engineering, transgenics, and gene editing of plants; b) microbe-mediated modifications involving genetic alterations of microbes through upstream or downstream methodologies; and c) soil amendments. These mechanisms shape the rhizospheric microbiome, making plants more productive and resilient under different stress conditions. This review paper comprehensively summarizes the various aspects of rhizosphere engineering and their potential applications in maintaining plant health and achieving optimum agricultural productivity.}, }
@article {pmid38007617, year = {2023}, author = {Umarje, SC and Banerjee, SK}, title = {Non-traditional approaches for control of antibiotic resistance.}, journal = {Expert opinion on biological therapy}, volume = {}, number = {}, pages = {1-23}, doi = {10.1080/14712598.2023.2279644}, pmid = {38007617}, issn = {1744-7682}, abstract = {INTRODUCTION: The drying up of antibiotic pipeline has necessitated the development of alternative therapeutic strategies to control the problem of antimicrobial resistance (AMR) that is expected to kill 10-million people annually by 2050. Newer therapeutic approaches address the shortcomings of traditional small-molecule antibiotics - the lack of specificity, evolvability, and susceptibility to mutation-based resistance. These 'non-traditional' molecules are biologicals having a complex structure and mode(s) of action that makes them resilient to resistance.<br><br>AREAS COVERED: This review aims to provide information about the non-traditional drug development approaches to tackle the problem of antimicrobial resistance, from the pre-antibiotic era to the latest developments. We have covered the molecules under development in the clinic with literature sourced from reviewed scholarly articles, official company websites involved in innovation of concerned therapeutics, press releases from the regulatory bodies, and clinical trial databases.<br><br>EXPERT OPINION: Formal introduction of non-traditional therapies in general practice can be quick and feasible only if supported with companion diagnostics and used in conjunction with established therapies. Owing to relatively higher development costs, non-traditional therapeutics require more funding as well as well as clarity in regulatory and clinical path. We are hopeful these issues are adequately addressed before AMR develops into a pandemic.}, }
@article {pmid38007500, year = {2023}, author = {Matthews, JL and Hoch, L and Raina, JB and Pablo, M and Hughes, DJ and Camp, EF and Seymour, JR and Ralph, PJ and Suggett, DJ and Herdean, A}, title = {Symbiodiniaceae photophysiology and stress resilience is enhanced by microbial associations.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {20724}, pmid = {38007500}, issn = {2045-2322}, mesh = {Animals ; *Anthozoa/physiology ; Photosynthesis ; Temperature ; Bacteria ; Photosystem II Protein Complex ; *Dinoflagellida/physiology ; Symbiosis ; }, abstract = {Symbiodiniaceae form associations with extra- and intracellular bacterial symbionts, both in culture and in symbiosis with corals. Bacterial associates can regulate Symbiodiniaceae fitness in terms of growth, calcification and photophysiology. However, the influence of these bacteria on interactive stressors, such as temperature and light, which are known to influence Symbiodiniaceae physiology, remains unclear. Here, we examined the photophysiological response of two Symbiodiniaceae species (Symbiodinium microadriaticum and Breviolum minutum) cultured under acute temperature and light stress with specific bacterial partners from their microbiome (Labrenzia (Roseibium) alexandrii, Marinobacter adhaerens or Muricauda aquimarina). Overall, bacterial presence positively impacted Symbiodiniaceae core photosynthetic health (photosystem II [PSII] quantum yield) and photoprotective capacity (non-photochemical quenching; NPQ) compared to cultures with all extracellular bacteria removed, although specific benefits were variable across Symbiodiniaceae genera and growth phase. Symbiodiniaceae co-cultured with M. aquimarina displayed an inverse NPQ response under high temperatures and light, and those with L. alexandrii demonstrated a lowered threshold for induction of NPQ, potentially through the provision of antioxidant compounds such as zeaxanthin (produced by Muricauda spp.) and dimethylsulfoniopropionate (DMSP; produced by this strain of L. alexandrii). Our co-culture approach empirically demonstrates the benefits bacteria can deliver to Symbiodiniaceae photochemical performance, providing evidence that bacterial associates can play important functional roles for Symbiodiniaceae.}, }
@article {pmid38007124, year = {2023}, author = {You, W and An, Q and Guo, D and Huang, Z and Guo, L and Chen, Z and Xu, H and Wang, G and Weng, Y and Ma, Z and Chen, X and Hong, F and Zhao, R}, title = {Exploration of risk analysis and elimination methods for a Cr(VI)-removal recombinant strain through a biosafety assessment in mice.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {168743}, doi = {10.1016/j.scitotenv.2023.168743}, pmid = {38007124}, issn = {1879-1026}, abstract = {Though recombinant strains are increasingly recognized for their potential in heavy metal remediation, few studies have evaluated their safety. Moreover, biosafety assessments of fecal-oral pathway exposure at country as well as global level have seldom analyzed the health risks of exposure to microorganisms from a microscopic perspective. The present study aimed to predict the long-term toxic effects of recombinant strains by conducting a subacute toxicity test on the chromium-removal recombinant strain 3458 and analyzing the gut microbiome. The available disinfection methods were also evaluated. The results showed that strain 3458 induced liver damage and affected renal function and lipid metabolism at 1.0 × 10[11] CFU/mL, which may be induced by its carrier strain, pET-28a. Strain 3458 poses the risk of increasing the number of pathogenic bacteria under prolonged exposure. When 500 mg L[-1] chlorine-containing disinfectant or 250 mg L[-1] chlorine dioxide disinfectant was added for 30 min, the sterilization rate exceeded 99.9 %. These findings suggest that existing wastewater disinfection methods can effectively sterilize strain 3458, ensuring its application value. The present study can serve a reference for the biosafety evaluation of the recombinant strain through exposure to the digestive tract and its feasibility for application in environmental pollution remediation.}, }
@article {pmid38007081, year = {2023}, author = {Tinkov, AA and Skalny, AV and Domingo, JL and Samarghandian, S and Kirichuk, AA and Aschner, M}, title = {A review of the epidemiological and laboratory evidence of the role of aluminum exposure in pathogenesis of cardiovascular diseases.}, journal = {Environmental research}, volume = {242}, number = {}, pages = {117740}, doi = {10.1016/j.envres.2023.117740}, pmid = {38007081}, issn = {1096-0953}, abstract = {The objective of the present study was to review the epidemiological and laboratory evidence on the role of aluminum (Al) exposure in the pathogenesis of cardiovascular diseases. Epidemiological data demonstrated an increased incidence of cardiovascular diseases (CVD), including hypertension and atherosclerosis in occupationally exposed subjects and hemodialysis patients. In addition, Al body burden was found to be elevated in patients with coronary heart disease, hypertension, and dyslipidemia. Laboratory studies demonstrated that Al exposure induced significant ultrastructural damage in the heart, resulting in electrocardiogram alterations in association with cardiomyocyte necrosis and apoptosis, inflammation, oxidative stress, inflammation, and mitochondrial dysfunction. In agreement with the epidemiological findings, laboratory data demonstrated dyslipidemia upon Al exposure, resulting from impaired hepatic lipid catabolism, as well as promotion of low-density lipoprotein oxidation. Al was also shown to inhibit paraoxonase 1 activity and to induce endothelial dysfunction and adhesion molecule expression, further promoting atherogenesis. The role of Al in hypertension was shown to be mediated by up-regulation of NADPH-oxidase, inhibition of nitric oxide bioavailability, and stimulation of renin-angiotensin-aldosterone system. It has been also demonstrated that Al exposure targets cerebral vasculature, which may be considered a link between Al exposure and cerebrovascular diseases. Findings from other tissues lend support that ferroptosis, pyroptosis, endoplasmic reticulum stress, and modulation of gut microbiome and metabolome are involved in the development of CVD upon Al exposure. A better understanding of the role of the cardiovascular system as a target for Al toxicity will be useful for risk assessment and the development of treatment and prevention strategies.}, }
@article {pmid38007045, year = {2023}, author = {Lin, CS and Chen, TC and Verhoeff, MC and Lobbezoo, F and Trulsson, M and Fuh, JL}, title = {An Umbrella Review on the Association between Factors of Oral Health and Cognitive Dysfunction.}, journal = {Ageing research reviews}, volume = {}, number = {}, pages = {102128}, doi = {10.1016/j.arr.2023.102128}, pmid = {38007045}, issn = {1872-9649}, abstract = {An increasing number of systematic reviews and meta-analyses have been published on the association between oral health and cognitive dysfunction, also known as oral-cognitive links. However, there is great diversity in the oral and cognitive factors included in these studies, with different opinions for clinical practice drawn from the evidence. To understand which oral and cognitive factors are involved in those associations, we conducted an umbrella review of 28 systematic reviews, including 12 meta-analyses, on oral-cognitive links. We found that (a) periodontal diseases, oral microbiome, and dementia were frequently studied, while other factors, such as mastication and mild cognitive impairment, were less commonly investigated, and (b) severe deterioration of oral health, such as severe periodontitis or extensive tooth loss, was strongly associated with cognitive dysfunction, rather than the presence of oral diseases alone. In conclusion, the diversity of oral and cognitive factors included in the review studies reflects the complexity of oral-cognitive links. Clarifying the factors helps to form evidence-based clinical advice for healthcare.}, }
@article {pmid38007009, year = {2023}, author = {Ravindran, DR and Kannan, S and Marudhamuthu, M}, title = {Fabrication and characterisation of human gut microbiome derived exopolysaccharide mediated silver nanoparticles - An in-vitro and in-vivo approach of Bio-Pm-AgNPs targeting Vibrio cholerae.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {128406}, doi = {10.1016/j.ijbiomac.2023.128406}, pmid = {38007009}, issn = {1879-0003}, abstract = {Utilising bacteria to produce silver nanoparticles was highly favoured due to its ability to minimise costs and mitigate any potential negative environmental impact. Exopolysaccharides (EPS) extracted from the human gut microbe have demonstrated remarkable efficacy in combating various bacterial infections. Exopolysaccharide (EPS), a naturally occurring biomolecule found in the human gut isolate Proteus mirabilis DMTMMR-11, was characterised using analytical techniques such as Fourier transform infrared spectroscopy (FTIR), [1]H-nuclear magnetic resonance, [13]C-nuclear magnetic resonance (NMR), and chemical composition analysis, which confirms the presence of carbohydrates (81.03 ± 0.23), proteins (4.22 ± 1.2), uronic acid (12.1 ± 0.12), and nucleic acid content (2.44 ± 0.15) in exopolysaccharide. The one factor at a time (OFAT) and response surface methodology (RSM) - central composite design (CCD) approaches were used to optimise the production of Bio-Pm-AgNPs, leading to an increase in yield of up to 1.86 g/L. The Bio-Pm-AgNPs were then subjected to Fourier transform infrared spectroscopy (FTIR) which determines the functional groups, X-ray diffractometer confers that Bio-Pm-AgNPs are crystalline in nature, field emission-scanning electron microscopy (FE-SEM) reveals the morphology of Bio-Pm-AgNPs, energy dispersive X-ray spectroscopy (EDX) confirms the presence of elements like Ag, C and O, high-resolution transmission electron microscopy (HR-TEM) determines that the Bio-Pm-AgNPs are sphere-shaped at 75 nm. Dynamic light scattering (DLS) and zeta potential analysis were also carried out to reveal the physiological nature of Bio-Pm-AgNPs. Bio-Pm-AgNPs have a promising effect on the inhibitory mechanism of Vibrio cholerae cells at a MIC concentration of 20 μg/ml which significantly affects cellular respiration and energy metabolism through glycolysis and TCA cycles by deteriorating the enzyme responsible for ATP and NADH utilisation. The action of Bio-Pm-AgNPs reduces the purity and concentration of nucleic acids, which leads to higher DNA damage. In-vivo analysis reveals that the treatment of Bio-Pm-AgNPs decreased the colonisation of V. cholerae and improved the survival rates in C. elegans.}, }
@article {pmid38006809, year = {2023}, author = {Wu, J and Zhang, HL and Guo, S and Li, X and Dong, T and Zhu, Y and Tsim, KWK}, title = {Acori Tatarinowii Rhizoma prevents the fluoxetine-induced multiple-drug resistance of Escherichia coli against antibiotics.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {123}, number = {}, pages = {155232}, doi = {10.1016/j.phymed.2023.155232}, pmid = {38006809}, issn = {1618-095X}, abstract = {BACKGROUND: In treating depression, the residual anti-depressant in gut interacts with the microbiome, leading to the appearance of multiple drug resistant (MDR) mutants, which poses a challenge for the treatment of infectious complications. Strategy is needed to combat this issue. Acori Tatarinowii Rhizoma (ATR, rhizome of Acorus tatarinowii Schott, Araceae), a traditional Chinese medicine, has been widely used for treatment of neurological disorders and gastrointestinal digestive disease in China. Here, ATR was demonstrated an excellent MDR-preventing effect in fluoxetine-induced Escherichia coli (E. coli).<br><br>AIM OF THE STUDY: This study aimed to reveal the effective role of ATR and its signaling cascades involved in preventing fluoxetine-induced MDR.<br><br>MATERIALS AND METHODS: The water extract of ATR was co-applied with sub-minimum inhibitory concentration (100&#xa0;mg/l) of fluoxetine in E. coli to evaluate its anti-MDR potential. Formation of reactive oxygen species (ROS) and expression of MDR-related genes in bacteria were measured by dichloro-dihydro-fluorescein diacetate assay and real-time PCR, respectively. Two fluorescent dyes, 1-N-phenylnapthylamine and 3,3'-dipropylthiadicarbocyanine were used to analyze the outer membrane permeability and inner membrane depolarization of E. coli. The accumulation of fluoxetine in the treated E. coli was determined via HPLC. The active fraction of ATR was identified.<br><br>RESULTS: The water extract of ATR significantly decreased the number of MDR mutants induced by fluoxetine and had half effective concentrations (EC50) of 55.5&#xa0;&#x3bc;g/ml and 16.8&#xa0;&#x3bc;g/ml for chloramphenicol and tetracycline, respectively. ATR robustly reversed the fluoxetine-induced superoxide response and membrane damage in E. coli. In addition, the inclusion of ATR significantly reduced the accumulation of fluoxetine in E. coli. After further fractionation, the polysaccharide of ATR was demonstrated as the fraction with the most significant anti-MDR activity.<br><br>CONCLUSIONS: This is the first report to investigate the MDR-preventing effect of ATR. The results of this study proposed ATR as an excellent herbal product to prevent MDR issues, as induced by fluoxetine, with the potential to reduce the side effects during the drug therapy of depression.}, }
@article {pmid38006744, year = {2023}, author = {Elgart, M and Zhang, Y and Zhang, Y and Yu, B and Kim, Y and Zee, PC and Gellman, MD and Boerwinkle, E and Daviglus, ML and Cai, J and Redline, S and Burk, RD and Kaplan, R and Sofer, T}, title = {Anaerobic pathogens associated with OSA may contribute to pathophysiology via amino-acid depletion.}, journal = {EBioMedicine}, volume = {98}, number = {}, pages = {104891}, doi = {10.1016/j.ebiom.2023.104891}, pmid = {38006744}, issn = {2352-3964}, abstract = {BACKGROUND: The human microbiome is linked to multiple metabolic disorders such as obesity and diabetes. Obstructive sleep apnoea (OSA) is a common sleep disorder with several metabolic risk factors. We investigated the associations between the gut microbiome composition and function, and measures of OSA severity in participants from a prospective community-based cohort study: the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).<br><br>METHODS: Bacterial-Wide Association Analysis (BWAS) of gut microbiome measured via metagenomics with OSA measures was performed adjusting for clinical, lifestyle and co-morbidities. This was followed by functional analysis of the OSA-enriched bacteria. We utilized additional metabolomic and transcriptomic associations to suggest possible mechanisms explaining the microbiome effects on OSA.<br><br>FINDINGS: Several uncommon anaerobic human pathogens were associated with OSA severity. These belong to the Lachnospira, Actinomyces, Kingella and Eubacterium genera. Functional analysis revealed enrichment in 49 processes including many anaerobic-related ones. Severe OSA was associated with the depletion of the amino acids glycine and glutamine in the blood, yet neither diet nor gene expression revealed any changes in the production or consumption of these amino acids.<br><br>INTERPRETATION: We show anaerobic bacterial communities to be a novel component of OSA pathophysiology. These are established in the oxygen-poor environments characteristic of OSA. We hypothesize that these bacteria deplete certain amino acids required for normal human homeostasis and muscle tone, contributing to OSA phenotypes. Future work should test this hypothesis as well as consider diagnostics via anaerobic bacteria detection and possible interventions via antibiotics and amino-acid supplementation.<br><br>FUNDING: Described in methods.}, }
@article {pmid38006743, year = {2023}, author = {Wei, J and Yang, Z and Li, J and Zhang, Y and Zhang, W and Doherty, M and Yang, T and Yang, Y and Li, H and Wang, Y and Wu, Z and Li, C and Lei, G and Zeng, C}, title = {Association between gut microbiome-related metabolites and symptomatic hand osteoarthritis in two independent cohorts.}, journal = {EBioMedicine}, volume = {98}, number = {}, pages = {104892}, doi = {10.1016/j.ebiom.2023.104892}, pmid = {38006743}, issn = {2352-3964}, abstract = {BACKGROUND: Since gut microbiome dysbiosis can cause inflammatory disorders by affecting host metabolism, we postulate that the gut microbiome and related metabolites could play a role in hand osteoarthritis. We characterised gut microbiome-related metabolites in people with symptomatic hand osteoarthritis (SHOA) in two independent cohorts.<br><br>METHODS: Using data collected from a large-sample community-based observational study (discovery cohort), we assessed the relations of the microbial function and plasma key metabolites related to altered microbial function with SHOA. Finally, we verified the relations of plasma metabolites to SHOA in an independent observational study (validation cohort).<br><br>FINDINGS: In the discovery cohort (n&#xa0;=&#xa0;1359), compared to those without SHOA, participants with SHOA had significantly altered microbial functions related to tryptophan metabolism (Q&#xa0;=&#xa0;0.025). Therefore we measured the plasma tryptophan metabolites and found that participants with SHOA had higher levels of 5-hydroxyindoleacetic acid (odds ratio [OR]&#xa0;=&#xa0;1.25, 95% confidence interval [CI]: 1.09-1.42) and 5-hydroxytryptophol (OR&#xa0;=&#xa0;1.13, 95% CI: 1.04-1.23), but lower levels of indole-3-lactic acid (ILA) (OR&#xa0;=&#xa0;0.85, 95% CI: 0.72-1.00), skatole (OR&#xa0;=&#xa0;0.93, 95% CI: 0.88-0.99) and 3-hydroxyanthranilic acid (OR&#xa0;=&#xa0;0.90, 95% CI: 0.85-0.96). Findings from the validation cohort (n&#xa0;=&#xa0;142) verified that lower levels of ILA were related to SHOA (OR&#xa0;=&#xa0;0.70, 95% CI: 0.53-0.92).<br><br>INTERPRETATION: Alterations of the microbial function of tryptophan biosynthesis and tryptophan metabolites, especially lower levels of ILA, are associated with SHOA. These findings suggest the role of the microbiome and tryptophan metabolites in developing of SHOA and may contribute to future translational opportunities.<br><br>FUNDING: National Key Research and Development Plan and National Natural Science Foundation of China.}, }
@article {pmid38006691, year = {2023}, author = {Hes, C and Desilets, A and Tonneau, M and El Ouarzadi, O and De Figueiredo Sousa, M and Bahig, H and Filion, &#xc9; and Nguyen-Tan, PF and Christopoulos, A and Benlaïfaoui, M and Derosa, L and Alves Costa Silva, C and Ponce, M and Malo, J and Belkad, W and Charpentier, D and Aubin, F and Hamilou, Z and Jamal, R and Messaoudene, M and Soulières, D and Routy, B}, title = {Gut microbiome predicts gastrointestinal toxicity outcomes from chemoradiation therapy in patients with head and neck squamous cell carcinoma.}, journal = {Oral oncology}, volume = {148}, number = {}, pages = {106623}, doi = {10.1016/j.oraloncology.2023.106623}, pmid = {38006691}, issn = {1879-0593}, abstract = {OBJECTIVES: Chemoradiation (CRT) in patients with locally advanced head and neck squamous cell cancer (HNSCC) is associated with significant toxicities, including mucositis. The gut microbiome represents an emerging hallmark of cancer and a potentially important biomarker for CRT-related adverse events. This prospective study investigated the association between the gut microbiome composition and CRT-related toxicities in patients with HNSCC, including mucositis.<br><br>MATERIALS AND METHODS: Stool samples from patients diagnosed with locally advanced HNSCC were prospectively collected prior to CRT initiation and analyzed using shotgun metagenomic sequencing to evaluate gut microbiome composition at baseline. Concurrently, clinicopathologic data, survival outcomes and the incidence and grading of CRT-emergent adverse events were documented in all patients.<br><br>RESULTS: A total of 52 patients were included, of whom 47 had baseline stool samples available for metagenomic analysis. Median age was 62, 83&#xa0;% patients were men and 54&#xa0;% had stage III-IV disease. All patients developed CRT-induced mucositis, including 42&#xa0;% with severe events (i.e. CTCAE v5.0 grade&#xa0;&#x2265;&#xa0;3) and 25&#xa0;% who required enteral feeding. With a median follow-up of 26.5 months, patients with severe mucositis had shorter overall survival (HR&#xa0;=&#xa0;3.3, 95&#xa0;%CI 1.0-10.6; p&#xa0;=&#xa0;0.02) and numerically shorter progression-free survival (HR&#xa0;=&#xa0;2.8, 95&#xa0;%CI, 0.8-9.6; p&#xa0;=&#xa0;0.09). The gut microbiome beta-diversity of patients with severe mucositis differed from patients with grades 1-2 mucositis (p&#xa0;=&#xa0;0.04), with enrichment in Mediterraneibacter (Ruminococcus gnavus) and Clostridiaceae family members, including Hungatella hathewayi. Grade 1-2 mucositis was associated with enrichment in Eubacterium rectale, Alistipes putredinis and Ruminococcaceae family members. Similar bacterial profiles were observed in patients who required enteral feeding.<br><br>CONCLUSION: Patients who developed severe mucositis had decreased survival and enrichment in specific bacteria associated with mucosal inflammation. Interestingly, these same bacteria have been linked to immune checkpoint inhibitor resistance.}, }
@article {pmid38006569, year = {2023}, author = {Aminu, S and Ascandari, A and Laamarti, M and Safdi, NEH and El Allali, A and Daoud, R}, title = {Exploring microbial worlds: a review of whole genome sequencing and its application in characterizing the microbial communities.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-25}, doi = {10.1080/1040841X.2023.2282447}, pmid = {38006569}, issn = {1549-7828}, abstract = {The classical microbiology techniques have inherent limitations in unraveling the complexity of microbial communities, necessitating the pivotal role of sequencing in studying the diversity of microbial communities. Whole genome sequencing (WGS) enables researchers to uncover the metabolic capabilities of the microbial community, providing valuable insights into the microbiome. Herein, we present an overview of the rapid advancements achieved thus far in the use of WGS in microbiome research. There was an upsurge in publications, particularly in 2021 and 2022 with the United States, China, and India leading the metagenomics research landscape. The Illumina platform has emerged as the widely adopted sequencing technology, whereas a significant focus of metagenomics has been on understanding the relationship between the gut microbiome and human health where distinct bacterial species have been linked to various diseases. Additionally, studies have explored the impact of human activities on microbial communities, including the potential spread of pathogenic bacteria and antimicrobial resistance genes in different ecosystems. Furthermore, WGS is used in investigating the microbiome of various animal species and plant tissues such as the rhizosphere microbiome. Overall, this review reflects the importance of WGS in metagenomics studies and underscores its remarkable power in illuminating the variety and intricacy of the microbiome in different environments.}, }
@article {pmid38006554, year = {2024}, author = {Walker, T}, title = {Detection of Natural Wolbachia Strains in Anopheles Mosquitoes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2739}, number = {}, pages = {205-218}, pmid = {38006554}, issn = {1940-6029}, mesh = {Animals ; Humans ; *Anopheles/genetics ; *Wolbachia/genetics ; In Situ Hybridization, Fluorescence ; Mosquito Vectors ; *Malaria ; }, abstract = {Wolbachia is an endosymbiotic bacterium that naturally infects many insect species, including mosquitoes that transmit human diseases. Wolbachia strains have been shown to inhibit the transmission of both arboviruses and malaria Plasmodium parasites. The existence of natural strains in wild Anopheles (An.) mosquitoes, the vectors of malaria parasites, in an endosymbiotic relationship is still to be fully determined. Although Wolbachia has been reported to be present in wild populations of the An. gambiae complex, the primary vectors of malaria in Sub-Saharan Africa, Wolbachia DNA sequence density and infection frequencies are low. As most studies have used highly sensitive nested PCR as the only detection method, more robust evidence is required to determine whether Wolbachia strains are established as endosymbionts in Anopheles species. Techniques such as fluorescent in situ hybridization, microbiome sequencing, and Wolbachia whole genome sequencing have provided concrete evidence for genuine Wolbachia strains in two mosquito species: An. moucheti and An. demeilloni. In this chapter, the current methodology used to determine if resident strains exist in Anopheles mosquitoes will be reviewed, including both PCR- and non-PCR-based protocols.}, }
@article {pmid38006513, year = {2023}, author = {Subbaiyan, R and Ganesan, A and Varadharajan, V and Jeyachandran, PR and Thangavel, H}, title = {Formulation and validation of probioticated foxtail millet laddu as a source of antioxidant for biological system using response surface methodology.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {38006513}, issn = {1678-4405}, abstract = {Probiotics play a critical role in supporting a healthy gut microbiome, which significantly impacts overall health and well-being. While there has been an increase in the availability of probiotic foods in recent years, there may still be limited options and accessibility in certain regions. This study focused on formulating a traditional Indian sweet called laddu enriched with millet and Lactobacillus acidophilus. The formulation of laddu ingredients was optimized using Design Expert software to create an optimal product for testing. The probiotic Lactobacillus acidophilus culture was incorporated into the laddu in three forms: lyophilized, microencapsulated powder, and natural curd. The probiotic foxtail laddu was selected based on specific criteria such as color, odor, and texture. The nutritional analysis revealed that the laddu contained approximately 64.46 g of carbohydrates, 15.13 g of protein, and 5.06 g of fat per 100 g of laddu. A microbial count analysis was performed over a two-month storage period to assess the viability of the incorporated Lactobacillus acidophilus. The results showed that the lyophilized and microencapsulated culture demonstrated good viability, with counts of 6.10 ± 0.09 log CFU/g and 7.43 ± 0.02 log CFU/g, respectively, when stored at 4 °C. In comparison, storage at room temperature resulted in counts of 5.41 ± 0.08 log CFU/g and 6.97 ± 0.02 log CFU/g at the end of the storage period. Based on the findings, the probiotic millet laddu developed in this study has the potential to be a value-added food product that can enhance the overall health of consumers. Incorporating probiotics into traditional food items like laddu offers a convenient and enjoyable way to promote gut health and improve the product's nutritional value.}, }
@article {pmid38006392, year = {2023}, author = {Zhou, P and Yan, H and Zhang, Y and Qi, R and Zhang, H and Liu, J}, title = {Growth performance, bile acid profile, fecal microbiome and serum metabolomics of growing-finishing pigs fed diets with bile acids supplementation.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skad393}, pmid = {38006392}, issn = {1525-3163}, abstract = {The present experiment was conducted to determine the effect of bile acids (BAs) supplementation on growth performance, BAs profile, fecal microbiome, and serum metabolomics in growing-finishing pigs. A total of 60 pigs [Duroc × (Landrace ×Yorkshire)] with an average body weight of 27.0 ± 1.5 kg were selected and allotted into one of 2 groups (castrated male to female ratio = 1:1), with 10 replicates per treatment and 3 pigs per replicate. The 2 treatments were the control group (Control) and a porcine bile extract supplemented group dosed at 0.5 g/kg feed (BA). After a 16-wk treatment, growth performance, BAs profiles in serum and feces and fecal microbial composition were determined. An untargeted metabolomics approach using gas chromatography with a time-of-flight mass spectrometer (GC-TOF-MS) was conducted to identify the metabolic pathways and associated metabolites in the serum of pigs. We found that BAs supplementation had no effect on the growth performance of the growing-finishing pig. However, it tended to increase the gain to feed ratio for the whole period (P = 0.07). Bile acids supplementation resulted in elevated serum concentrations of secondary BAs (SBA), including hyodeoxycholic acid (HDCA), glycoursodeoxycholic acid (GUDCA), and tauro-hyodeoxycholic acid (THDCA), as well as fecal concentration of HDCA (P < 0.05). Fecal microbiota analysis revealed no differences in alpha and beta diversity indices or the relative abundance of Operational Taxonomic Units (OTUs) at both phylum and genus levels between groups. Metabolic pathway analysis revealed that the differential metabolites between Control and BA groups mainly involved in purine metabolism, ether lipid metabolism, glycerophospholipid metabolism, and amino sugar and nucleotide sugar metabolism, as well as primary bile acid biosynthesis. Our findings indicate that BAs supplementation tended to improve the feed efficiency, and significantly altered the BA profile in the serum and feces of growing-finished pigs, regardless of any changes in the gut microbial composition. The altered metabolic pathways could potentially play a vital role in improving the feed efficiency of growing-finished pigs with BAs supplementation.}, }
@article {pmid38006234, year = {2023}, author = {Yadav, A and Ahlawat, S and Sharma, KK}, title = {Culturing the unculturables: strategies, challenges, and opportunities for gut microbiome study.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxad280}, pmid = {38006234}, issn = {1365-2672}, abstract = {Metagenome sequencing techniques revolutionized the field of gut microbiome study. However, it is equipped with experimental and computational biases which affect the downstream analysis results. Also, live microbial strains is needed for a better understanding of host-microbial crosstalks and for designing next-generation treatment therapies based on probiotic strains and postbiotic molecules. Conventional culturing methodologies are insufficient to get the dark gut matter on the plate; therefore, there is an urgent need to propose novel culturing methods that can fill the limitations of metagenomic. The current work aims to provide a consolidated evaluation of the available methods for host-microbe interaction with an emphasis on in vitro culturing of gut microbes using organoids, gut on a chip, and gut bioreactor. Further, the knowledge of microbial crosstalk in the gut helps us to identify core microbiota, and key metabolites that will aid in designing culturing media and co-culturing systems for gut microbiome study. After the deeper mining of the current culturing methods, we recommend that 3-D printed intestinal cells in a multistage continuous flow reactor equipped with an extended organoid system might be a good practical choice for gut microbiota-based studies.}, }
@article {pmid38005959, year = {2023}, author = {Balieiro Neto, G and Engracia Filho, JR and Budino, FEL and Freitas, AWP and Soares, WVB}, title = {Effects of High-Biotin Sample Interference on Antibody Concentrations in Sandwich Immunoassays.}, journal = {Vaccines}, volume = {11}, number = {11}, pages = {}, pmid = {38005959}, issn = {2076-393X}, abstract = {The use of antimicrobial growth promoters (AGPs) is banned because of problems associated with drug residues in animal products and increased bacterial resistance. The immunization of chickens with specific antigens is a promising strategy for generating specific antibodies that can target a wide range of antibiotic-resistant bacteria and can be used as an alternative to antibiotics. Immunoglobulin Y (IgY) antibodies in a polyclonal antibody (pAb) format, when administered orally, modulate the ruminal microbiome and maintain animal health and performance; however, there are concerns pertaining to protein impurities and biotin concentrations in the samples. Signal amplification strategies involving the noncovalent interaction of biotin with streptavidin is extensively used in diagnosis and scientific research, particularly in enzyme-linked immunosorbent assays (ELISAs). However, the high concentrations of biotin in samples, especially in those derived from rich sources such as egg yolk, can pose challenges and potentially harm the accuracy of diagnostic tests and protein concentration measurements. This study aimed to evaluate the influence of biotin on the measurement of IgY in freeze-dried egg yolk samples obtained from immunized laying hens using immunoassays with biotin-avidin/streptavidin. The detection of IgY in yolk samples using ELISA with streptavidin-biotin binding could lead to misdiagnosis due to biotin interference; the level of interference varies with the specific assay conditions and the concentration of biotin in the yolk samples. An ELISA without streptavidin-biotin binding is advisable to avoid interactions between biotin and target proteins, prevent biotin interference with the results, and achieve more reliable and accurate results.}, }
@article {pmid38005873, year = {2023}, author = {Borase, H and Shukla, D}, title = {The Interplay of Genital Herpes with Cellular Processes: A Pathogenesis and Therapeutic Perspective.}, journal = {Viruses}, volume = {15}, number = {11}, pages = {}, pmid = {38005873}, issn = {1999-4915}, support = {R01AI139768//National Institute of Health/ ; }, mesh = {Humans ; *Herpes Genitalis/drug therapy/pathology ; Herpesvirus 2, Human/physiology ; Autophagy ; Antiviral Agents/pharmacology/therapeutic use ; *Herpes Simplex/drug therapy ; }, abstract = {Genital herpes, primarily caused by herpes simplex virus-2 (HSV-2), remains a pressing global health concern. Its remarkable ability to intertwine with cellular processes, from harnessing host machinery for replication to subverting antiviral defenses like autophagy and programmed cell death, exemplifies the intricate interplay at the heart of its pathogenesis. While the biomedical community has extensively researched antiviral interventions, the efficiency of these strategies in managing HSV-2 remains suboptimal. Recognizing this, attention has shifted toward leveraging host cellular components to regulate HSV-2 replication and influence the cell cycle. Furthermore, innovative interventional strategies-including drug repurposing, microbivacs, connecting the host microbiome, and exploiting natural secondary metabolites-are emerging as potential game changers. This review summarizes the key steps in HSV-2 pathogenesis and newly discovered cellular interactions, presenting the latest developments in the field, highlighting existing challenges, and offering a fresh perspective on HSV-2's pathogenesis and the potential avenues for its treatment by targeting cellular proteins and pathways.}, }
@article {pmid38004827, year = {2023}, author = {Kim, J and Koh, H}, title = {MiTree: A Unified Web Cloud Analytic Platform for User-Friendly and Interpretable Microbiome Data Mining Using Tree-Based Methods.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004827}, issn = {2076-2607}, support = {2021R1C1C1013861//National Research Foundation of Korea/ ; }, abstract = {The advent of next-generation sequencing has greatly accelerated the field of human microbiome studies. Currently, investigators are seeking, struggling and competing to find new ways to diagnose, treat and prevent human diseases through the human microbiome. Machine learning is a promising approach to help such an effort, especially due to the high complexity of microbiome data. However, many of the current machine learning algorithms are in a "black box", i.e., they are difficult to understand and interpret. In addition, clinicians, public health practitioners and biologists are not usually skilled at computer programming, and they do not always have high-end computing devices. Thus, in this study, we introduce a unified web cloud analytic platform, named MiTree, for user-friendly and interpretable microbiome data mining. MiTree employs tree-based learning methods, including decision tree, random forest and gradient boosting, that are well understood and suited to human microbiome studies. We also stress that MiTree can address both classification and regression problems through covariate-adjusted or unadjusted analysis. MiTree should serve as an easy-to-use and interpretable data mining tool for microbiome-based disease prediction modeling, and should provide new insights into microbiome-based diagnostics, treatment and prevention. MiTree is an open-source software that is available on our web server.}, }
@article {pmid38004817, year = {2023}, author = {Parigi, TL and Vieujean, S and Paridaens, K and Dalgaard, K and Peyrin-Biroulet, L and Danese, S}, title = {Efficacy, Safety, and Concerns on Microbiota Modulation, Antibiotics, Probiotics, and Fecal Microbial Transplant for Inflammatory Bowel Disease and Other Gastrointestinal Conditions: Results from an International Survey.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004817}, issn = {2076-2607}, abstract = {The gut microbiota play a pivotal role in human health. Dysbiosis, alterations in microbiota composition and function, is associated with gastrointestinal disorders, including inflammatory bowel disease (IBD). This international survey aimed to assess physicians' experiences, perceptions, and practices related to microbiome modulation for gastrointestinal conditions, with a focus on IBD. Results from 142 healthcare professionals, predominantly gastroenterologists, confirmed a consensus on the relevance of the gut microbiota in IBD pathogenesis. However, the utilization of microbial composition analysis and probiotics in clinical practice was limited, primarily due to the lack of standardized guidelines and supporting evidence. Physicians held conflicting views on antibiotics, recognizing their potential for inducing remission but also causing flares in IBD. Respondents also had varying opinions on the efficacy of fecal microbiota transplantation (FMT) for different gastrointestinal conditions, with higher confidence in FMT effectiveness for irritable bowel syndrome with diarrhea, pouchitis, and ulcerative colitis. Concerns on FMT included uncertainty about effect duration, administration intervals, and conflicting evidence. Donor selection was believed to be a crucial factor in FMT outcomes. This survey highlights the need for further research and evidence-based guidelines to optimize the use of microbiome-based therapies in clinical practice. As our understanding of the gut microbiome continues to evolve, these insights will contribute to more informed and personalized approaches to managing gastrointestinal disorders.}, }
@article {pmid38004804, year = {2023}, author = {Borrel, G and Fadhlaoui, K and Ben Hania, W and Gaci, N and Pehau-Arnaudet, G and Chaudhary, PP and Vandekerckove, P and Ballet, N and Alric, M and O'Toole, PW and Fardeau, ML and Ollivier, B and Brugère, JF}, title = {Methanomethylophilus alvi gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order Methanomassiliicoccales Isolated from the Human Gut and Proposal of the Novel Family Methanomethylophilaceae fam. nov.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004804}, issn = {2076-2607}, support = {NA/SFI_/Science Foundation Ireland/Ireland ; }, abstract = {The methanogenic strain Mx-05[T] was isolated from the human fecal microbiome. A phylogenetic analysis based on the 16S rRNA gene and protein marker genes indicated that the strain is affiliated with the order Methanomassiliicoccales. It shares 86.9% 16S rRNA gene sequence identity with Methanomassiliicoccus luminyensis, the only member of this order previously isolated. The cells of Mx-05[T] were non-motile cocci, with a diameter range of 0.4-0.7 μm. They grew anaerobically and reduced methanol, monomethylamine, dimethylamine, and trimethylamine into methane, using H2 as an electron donor. H2/CO2, formate, ethanol, and acetate were not used as energy sources. The growth of Mx-05[T] required an unknown medium factor(s) provided by Eggerthella lenta and present in rumen fluid. Mx-05[T] grew between 30 °C and 40 °C (optimum 37 °C), over a pH range of 6.9-8.3 (optimum pH 7.5), and between 0.02 and 0.34 mol.L[-1] NaCl (optimum 0.12 mol.L[-1] NaCl). The genome is 1.67 Mbp with a G+C content of 55.5 mol%. Genome sequence annotation confirmed the absence of the methyl branch of the H4MPT Wood-Ljungdahl pathway, as described for other Methanomassiliicoccales members. Based on an average nucleotide identity analysis, we propose strain Mx-05[T] as being a novel representative of the order Methanomassiliicoccales, within the novel family Methanomethylophilaceae, for which the name Methanomethylophilus alvi gen. nov, sp. nov. is proposed. The type strain is Mx-05[T] (JCM 31474T).}, }
@article {pmid38004800, year = {2023}, author = {Maddock, D and Brady, C and Denman, S and Arnold, D}, title = {Bacteria Associated with Acute Oak Decline: Where Did They Come From? We Know Where They Go.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004800}, issn = {2076-2607}, support = {BB/T010886/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Acute oak decline is a high-impact disease causing necrotic lesions on the trunk, crown thinning and the eventual death of oak. Four bacterial species are associated with the lesions-Brenneria goodwinii, Gibbsiella quercinecans, Rahnella victoriana and Lonsdalea Britannica-although an epi-/endophytic lifestyle has also been suggested for these bacteria. However, little is known about their environmental reservoirs or their pathway to endophytic colonisation. This work aimed to investigate the ability of the four AOD-associated bacterial species to survive for prolonged periods within rhizosphere soil, leaves and acorns in vitro, and to design an appropriate method for their recovery. This method was trialled on field samples related to healthy and symptomatic oaks. The in vitro study showed that the majority of these species could survive for at least six weeks within each sample type. Results from the field samples demonstrated that R. victoriana and G. quercinecans appear environmentally widespread, indicating multiple routes of endophytic colonisation might be plausible. B. goodwinii and L. britannica were only identified from acorns from healthy and symptomatic trees, indicating they may be inherited members of the endophytic seed microbiome and, despite their ability to survive outside of the host, their environmental occurrence is limited. Future research should focus on preventative measures targeting the abiotic factors of AOD, how endophytic bacteria shift to a pathogenic cycle and the identification of resilient seed stock that is less susceptible to AOD.}, }
@article {pmid38004795, year = {2023}, author = {Wallen-Russell, C and Pearlman, N and Wallen-Russell, S and Cretoiu, D and Thompson, DC and Voinea, SC}, title = {A Catastrophic Biodiversity Loss in the Environment Is Being Replicated on the Skin Microbiome: Is This a Major Contributor to the Chronic Disease Epidemic?.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004795}, issn = {2076-2607}, abstract = {There has been a catastrophic loss of biodiversity in ecosystems across the world. A similar crisis has been observed in the human gut microbiome, which has been linked to "all human diseases affecting westernized countries". This is of great importance because chronic diseases are the leading cause of death worldwide and make up 90% of America's healthcare costs. Disease development is complex and multifactorial, but there is one part of the body's interlinked ecosystem that is often overlooked in discussions about whole-body health, and that is the skin microbiome. This is despite it being a crucial part of the immune, endocrine, and nervous systems and being continuously exposed to environmental stressors. Here we show that a parallel biodiversity loss of 30-84% has occurred on the skin of people in the developed world compared to our ancestors. Research has shown that dysbiosis of the skin microbiome has been linked to many common skin diseases and, more recently, that it could even play an active role in the development of a growing number of whole-body health problems, such as food allergies, asthma, cardiovascular diseases, and Parkinson's, traditionally thought unrelated to the skin. Damaged skin is now known to induce systemic inflammation, which is involved in many chronic diseases. We highlight that biodiversity loss is not only a common finding in dysbiotic ecosystems but also a type of dysbiosis. As a result, we make the case that biodiversity loss in the skin microbiome is a major contributor to the chronic disease epidemic. The link between biodiversity loss and dysbiosis forms the basis of this paper's focus on the subject. The key to understanding why biodiversity loss creates an unhealthy system could be highlighted by complex physics. We introduce entropy to help understand why biodiversity has been linked with ecosystem health and stability. Meanwhile, we also introduce ecosystems as being governed by "non-linear physics" principles-including chaos theory-which suggests that every individual part of any system is intrinsically linked and implies any disruption to a small part of the system (skin) could have a significant and unknown effect on overall system health (whole-body health). Recognizing the link between ecosystem health and human health allows us to understand how crucial it could be to maintain biodiversity across systems everywhere, from the macro-environment we inhabit right down to our body's microbiome. Further, in-depth research is needed so we can aid in the treatment of chronic diseases and potentially change how we think about our health. With millions of people currently suffering, research to help mitigate the crisis is of vital importance.}, }
@article {pmid38004791, year = {2023}, author = {Thamm, M and Reiß, F and Sohl, L and Gabel, M and Noll, M and Scheiner, R}, title = {Solitary Bees Host More Bacteria and Fungi on Their Cuticle than Social Bees.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004791}, issn = {2076-2607}, support = {ID73253//Bayerisches Staatsministerium f&#xfc;r Umwelt und Verbraucherschutz/ ; }, abstract = {Bees come into contact with bacteria and fungi from flowering plants during their foraging trips. The Western honeybee (Apis mellifera) shows a pronounced hygienic behavior with social interactions, while the solitary red mason bee (Osmia bicornis) lacks a social immune system. Since both visit the same floral resources, it is intriguing to speculate that the body surface of a solitary bee should harbor a more complex microbiome than that of the social honeybee. We compared the cuticular microbiomes of A. mellifera (including three European subspecies) and O. bicornis for the first time by bacterial 16S rRNA and fungal ITS gene-based high-throughput amplicon sequencing. The cuticular microbiome of the solitary O. bicornis was significantly more complex than that of the social A. mellifera. The microbiome composition of A. mellifera subspecies was very similar. However, we counted significantly different numbers of fungi and a higher diversity in the honeybee subspecies adapted to warmer climates. Our results suggest that the cuticular microbiome of bees is strongly affected by visited plants, lifestyle and adaptation to temperature, which have important implications for the maintenance of the health of bees under conditions of global change.}, }
@article {pmid38004785, year = {2023}, author = {Zheng, W and Guan, Y and Wu, B}, title = {Effects of Yupingfeng Polysaccharides as Feed Supplement on Immune Function and Intestinal Microbiome in Chickens.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004785}, issn = {2076-2607}, support = {2019B030301010//Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding/ ; }, abstract = {The health of chicks is closely related to their productivity. Yupingfeng polysaccharide (YPF-P) is a kind of water-soluble polysaccharide extracted from Yupingfeng powder; it has high pharmacological activity and can be used as a potential substitute for antibiotics to improve the health of chicks. This study aimed to investigate the effects of YPF-P on immune performance, the duodenum, and the cecal microflora of chicks. All chickens (4224) were randomly distributed into four groups (eight replicas/group, 132 hens/replica). The control group was fed a basal diet (0 g/kg YPF-P), while the experimental groups were fed basal diets supplemented with 1, 2, or 4 g/kg YPF-P. The results showed that YPF-P significantly increased the thymus index (p < 0.05). The content of total antioxidant capacity (T-AOC), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), immunoglobulin A (IgA), and IgG and immunoglobulin M (IgM) was upregulated in the serum by YPF-P (p < 0.05). YPF-P decreased the content of malondialdehyde (MDA) (p < 0.05). Further, 16S rRNA sequencing showed that 2 g/kg YPF-P modulated the predominant duodenum and cecal microbial community structure, which increased the number of Faecalibacterium, Megamonas, Bacteroides, Alistipes, NK4A214_group, and Enterococcus. In conclusion, YPF-P ameliorated the growth performance of chicks by regulating serum immune and antioxidant balance, as well as the intestinal microbiota.}, }
@article {pmid38004775, year = {2023}, author = {Santiago, JM and Hallman, LM and Fox, JP and Pitino, M and Shatters, RG and Cano, LM and Rossi, L}, title = {Impacts of Oak Mulch Amendments on Rhizosphere Microbiome of Citrus Trees Grown in Florida Flatwood Soils.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004775}, issn = {2076-2607}, support = {#2019-38640-29878//United States Department of Agriculture/ ; #2020-70029-33176//United States Department of Agriculture/ ; UF/IFAS A.H. Krezdorn Memorial Fund//University of Florida/ ; }, abstract = {Rhizosphere interactions are an understudied component of citrus production. This is even more important in Florida flatwood soils, which pose significant challenges in achieving sustainable and effective fruit production due to low natural fertility and organic matter. Citrus growers apply soil amendments, including oak mulch, to ameliorate their soil conditions. Thus, the aim of this research was to evaluate the effects of oak mulch on citrus nutrient uptake, soil characteristics, and rhizosphere composition. The plant material consisted of 'Valencia' sweet orange (Citrus × sinensis) trees grafted on 'US-812' (C. reticulata × C. trifoliata) rootstock. The experiment consisted of two treatments, which included trees treated with oak mulch (300 kg of mulch per plot) and a control. The soil and leaf nutrient contents, soil pH, cation exchange capacity, moisture, temperature, and rhizosphere bacterial compositions were examined over the course of one year (spring and fall 2021). During the spring samplings, the citrus trees treated with oak mulch resulted in significantly greater soil Zn and Mn contents, greater soil moisture, and greater rhizosphere bacterial diversity compared to the control, while during the fall samplings, only a greater soil moisture content was observed in the treated trees. The soil Zn and Mn content detected during the spring samplings correlated with the significant increases in the diversity of the rhizosphere bacterial community composition. Similarly, the reduced rates of leaching and evaporation (at the soil surface) of oak mulch applied to Florida sandy soils likely played a large role in the significant increase in moisture and nutrient retention.}, }
@article {pmid38004761, year = {2023}, author = {Do, KH and Ko, SH and Kim, KB and Seo, K and Lee, WK}, title = {Comparative Study of Intestinal Microbiome in Patients with Ulcerative Colitis and Healthy Controls in Korea.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004761}, issn = {2076-2607}, support = {2021RIS-001//National Research Foundation of Korea/ ; }, abstract = {Ulcerative colitis (UC) poses a contemporary medical challenge, with its exact cause still eluding researchers. This is due to various factors, such as the rising incidence, diagnostic complexities, and difficulties associated with its management. We compared the intestinal microbiome of patients with UC to that of healthy controls to determine the qualitative and quantitative changes associated with UC that occur in the intestinal microbiota. The intestinal bacterial abundance in 40 Korean patients with UC and 25 healthy controls was assayed using via next-generation sequencing. There were five major phyla in both groups: Firmicutes (UC patients: 51.12%; healthy controls: 46.90%), Bacteroidota (UC patients: 37.04%; healthy controls: 40.34%), Proteobacteria (UC patients: 6.01%; healthy controls: 11.05%), Actinobacteriota (UC patients: 5.71%; healthy controls: 1.56%), and Desulfobacteriota (UC patients: 0.13%; healthy controls: 0.14%). Firmicutes was more prevalent in patients with UC (51.12%) compared to that of healthy controls (46.90%). Otherwise, Bacteroidota was more prevalent in healthy controls (40.34%) compared to patients with UC (37.04%). Although there was no significant difference, our results showed a substantially lower gut microbiome diversity in patients with UC (mean: 16.5; 95% confidence interval (CI) = 14.956-18.044) than in healthy controls (mean: 17.84; 95% CI = 15.989-19.691), the beta diversity and the flora structure of the microbiome in patients with UC differed from those in healthy controls. This will be helpful for the development of new treatment options and lay the groundwork for future research on UC. To understand the disease mechanism, it is essential to define the different types of microbes in the guts of patients with UC.}, }
@article {pmid38004758, year = {2023}, author = {Yan, P and Luo, S and Guo, L and Wang, X and Ren, X and Lv, J and Chen, Y and Lin, X and Chen, J and Wang, R}, title = {Unraveling Intestinal Microbial Shifts in ESRD and Kidney Transplantation: Implications for Disease-Related Dysbiosis.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004758}, issn = {2076-2607}, support = {82070766//National Natural Science Foundation of China/ ; 2022RC147//Medical Health Science and Technology Project of Zhejiang Provincial Health Commission/ ; LQ23H050003//Zhejiang Provincial Natural Science Foundation of China/ ; }, abstract = {The composition of the gut microbiome is profoundly influenced by the accumulation of toxins in end-stage renal disease (ESRD) and specific medical treatments during kidney transplantation (KT). However, variations in results may arise due to factors such as genetics, dietary habits, and the strategy of anti-rejection therapy. Therefore, we conducted a 16S rRNA sequencing study to characterize intestinal microbiomes by using 75 fecal specimens obtained from 25 paired Chinese living donors (LDs) of kidneys and recipients before and after KT. Surprisingly, similar enterotypes were observed between healthy LDs and ESRD recipients. Nonetheless, following KT, the fecal communities of recipients exhibited distinct clustering, which was primarily characterized by Escherichia-Shigella and Streptococcus at the genus level, along with a reduction in the diversity of microbiota. To further explore the characteristics of gut microorganisms in early rejection episodes, two recipients with biopsy-proven borderline changes during follow-up were enrolled in a preliminary sub-cohort study. Our findings reveal a comparable construction of gut microbiota between ESRD patients and their healthy relatives while also highlighting the significant impact of KT on gut microbial composition.}, }
@article {pmid38004757, year = {2023}, author = {Aryee, G and Luecke, SM and Dahlen, CR and Swanson, KC and Amat, S}, title = {Holistic View and Novel Perspective on Ruminal and Extra-Gastrointestinal Methanogens in Cattle.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004757}, issn = {2076-2607}, support = {N/A//North Dakota Agricultural Experiment Station/ ; }, abstract = {Despite the extensive research conducted on ruminal methanogens and anti-methanogenic intervention strategies over the last 50 years, most of the currently researched enteric methane (CH4) abatement approaches have shown limited efficacy. This is largely because of the complex nature of animal production and the ruminal environment, host genetic variability of CH4 production, and an incomplete understanding of the role of the ruminal microbiome in enteric CH4 emissions. Recent sequencing-based studies suggest the presence of methanogenic archaea in extra-gastrointestinal tract tissues, including respiratory and reproductive tracts of cattle. While these sequencing data require further verification via culture-dependent methods, the consistent identification of methanogens with relatively greater frequency in the airway and urogenital tract of cattle, as well as increasing appreciation of the microbiome-gut-organ axis together highlight the potential interactions between ruminal and extra-gastrointestinal methanogenic communities. Thus, a traditional singular focus on ruminal methanogens may not be sufficient, and a holistic approach which takes into consideration of the transfer of methanogens between ruminal, extra-gastrointestinal, and environmental microbial communities is of necessity to develop more efficient and long-term ruminal CH4 mitigation strategies. In the present review, we provide a holistic survey of the methanogenic archaea present in different anatomical sites of cattle and discuss potential seeding sources of the ruminal methanogens.}, }
@article {pmid38004753, year = {2023}, author = {Mathlouthi, NEH and Belguith, I and Yengui, M and Oumarou Hama, H and Lagier, JC and Ammar Keskes, L and Grine, G and Gdoura, R}, title = {The Archaeome's Role in Colorectal Cancer: Unveiling the DPANN Group and Investigating Archaeal Functional Signatures.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004753}, issn = {2076-2607}, abstract = {BACKGROUND AND AIMS: Gut microbial imbalances are linked to colorectal cancer (CRC), but archaea's role remains underexplored. Here, using previously published metagenomic data from different populations including Austria, Germany, Italy, Japan, China, and India, we performed bioinformatic and statistical analysis to identify archaeal taxonomic and functional signatures related to CRC.<br><br>METHODS: We analyzed published fecal metagenomic data from 390 subjects, comparing the archaeomes of CRC and healthy individuals. We conducted a biostatistical analysis to investigate the relationship between Candidatus Mancarchaeum acidiphilum (DPANN superphylum) and other archaeal species associated with CRC. Using the Prokka tool, we annotated the data focusing on archaeal genes, subsequently linking them to CRC and mapping them against UniprotKB and GO databases for specific archaeal gene functions.<br><br>RESULTS: Our analysis identified enrichment of methanogenic archaea in healthy subjects, with an exception for Methanobrevibacter smithii, which correlated with CRC. Notably, CRC showed a strong association with archaeal species, particularly Natrinema sp. J7-2, Ferroglobus placidus, and Candidatus Mancarchaeum acidiphilum. Furthermore, the DPANN archaeon exhibited a significant correlation with other CRC-associated archaea (p < 0.001). Functionally, we found a marked association between MvhB-type polyferredoxin and colorectal cancer. We also highlighted the association of archaeal proteins involved in the biosynthesis of leucine and the galactose metabolism process with the healthy phenotype.<br><br>CONCLUSIONS: The archaeomes of CRC patients show identifiable alterations, including a decline in methanogens and an increase in Halobacteria species. MvhB-type polyferredoxin, linked with CRC and species like Candidatus Mancarchaeum acidiphilum, Natrinema sp. J7-2, and Ferroglobus placidus emerge as potential archaeal biomarkers. Archaeal proteins may also offer gut protection, underscoring archaea's role in CRC dynamics.}, }
@article {pmid38004740, year = {2023}, author = {Ossa-Trujillo, C and Taylor, EA and Sarwar, F and Vinasco, J and Jordan, ER and Buitrago, JAG and Hagevoort, GR and Lawhon, SD and Piñeiro, JM and Galloway-Peña, J and Norman, KN and Scott, HM}, title = {Two-Dose Ceftiofur Treatment Increases Cephamycinase Gene Quantities and Fecal Microbiome Diversity in Dairy Cows Diagnosed with Metritis.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004740}, issn = {2076-2607}, support = {2016-68003- 24607//United States Department of Agriculture/ ; }, abstract = {Antimicrobial resistance is a significant concern worldwide; meanwhile, the impact of 3rd generation cephalosporin (3GC) antibiotics on the microbial communities of cattle and resistance within these communities is largely unknown. The objectives of this study were to determine the effects of two-dose ceftiofur crystalline-free acid (2-CCFA) treatment on the fecal microbiota and on the quantities of second-and third-generation cephalosporin, fluoroquinolone, and macrolide resistance genes in Holstein-Friesian dairy cows in the southwestern United States. Across three dairy farms, 124 matched pairs of cows were enrolled in a longitudinal study. Following the product label regimen, CCFA was administered on days 0 and 3 to cows diagnosed with postpartum metritis. Healthy cows were pair-matched based on lactation number and calving date. Fecal samples were collected on days 0, 6, and 16 and pooled in groups of 4 (n = 192) by farm, day, and treatment group for community DNA extraction. The characterization of community DNA included real-time PCR (qPCR) to quantify the following antibiotic resistance genes: blaCMY-2, blaCTX-M, mphA, qnrB19, and the highly conserved 16S rRNA back-calculated to gene copies per gram of feces. Additionally, 16S rRNA amplicon sequencing and metagenomics analyses were used to determine differences in bacterial community composition by treatment, day, and farm. Overall, blaCMY-2 gene copies per gram of feces increased significantly (p ≤ 0.05) in the treated group compared to the untreated group on day 6 and remained elevated on day 16. However, blaCTX-M, mphA, and qnrB19 gene quantities did not differ significantly (p ≥ 0.05) between treatment groups, days, or farms, suggesting a cephamycinase-specific enhancement in cows on these farms. Perhaps unexpectedly, 16S rRNA amplicon metagenomic analyses showed that the fecal bacterial communities from treated animals on day 6 had significantly greater (p ≤ 0.05) alpha and beta diversity than the untreated group. Two-dose ceftiofur treatment in dairy cows with metritis elevates cephamycinase gene quantities among all fecal bacteria while paradoxically increasing microbial diversity.}, }
@article {pmid38004716, year = {2023}, author = {Ahmed, RO and Ali, A and Leeds, T and Salem, M}, title = {Fecal Microbiome Analysis Distinguishes Bacterial Taxa Biomarkers Associated with Red Fillet Color in Rainbow Trout.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004716}, issn = {2076-2607}, support = {2021-67015-33388, 2023-67015-39742//National Institute of Food and Agriculture/ ; CRIS Project 8082-31000-013//United States Department of Agriculture, Agricultural Research Service/ ; }, abstract = {The characteristic reddish-pink fillet color of rainbow trout is an important marketing trait. The gastrointestinal microbiome is vital for host health, immunity, and nutrient balance. Host genetics play a crucial role in determining the gut microbiome, and the host-microbiome interaction impacts the host's phenotypic expression. We hypothesized that fecal microbiota could be used to predict fillet color in rainbow trout. Fish were fed Astaxanthin-supplemented feed for six months, after which 16s rDNA sequencing was used to investigate the fecal microbiome composition in rainbow trout families with reddish-pink fillet coloration (red fillet group, average saturation index = 26.50 ± 2.86) compared to families with pale white fillet color (white fillet group, average saturation index = 21.21 ± 3.53). The linear discriminant analysis effect size (LEFse) tool was used to identify bacterial biomarkers associated with fillet color. The alpha diversity measure shows no difference in the red and white fillet groups. Beta diversity principal component analysis showed clustering of the samples along the white versus red fillet group. The red fillet group has enrichment (LDA score > 1.5) of taxa Leuconostoc lactis, Corynebacterium variabile, Jeotgalicoccus halotolerans, and Leucobacter chromiireducens. In contrast, the white fillet group has an enriched presence of mycoplasma, Lachnoclostridium, and Oceanobacillus indicireducens. The enriched bacterial taxa in the red fillet group have probiotic functions and can generate carotenoid pigments. Bacteria taxa enriched in the white fillet group are either commensal, parasitic, or capable of reducing indigo dye. The study identified specific bacterial biomarkers differentially abundant in fish families of divergent fillet color that could be used in genetic selection to improve feed carotenoid retention and reddish-pink fillet color. This work extends our understanding of carotenoid metabolism in rainbow trout through the interaction between gut microbiota and fillet color.}, }
@article {pmid38004715, year = {2023}, author = {Bourumeau, W and Tremblay, K and Jourdan, G and Girard, C and Laprise, C}, title = {Bacterial Biomarkers of the Oropharyngeal and Oral Cavity during SARS-CoV-2 Infection.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004715}, issn = {2076-2607}, support = {2021-HQ-000051//Fonds de recherche du Qu&#xe9;bec - sant&#xe9; (FRQS) and Public Health Agency of Canada/ ; }, abstract = {(1) Background: Individuals with COVID-19 display different forms of disease severity and the upper respiratory tract microbiome has been suggested to play a crucial role in the development of its symptoms. (2) Methods: The present study analyzed the microbial profiles of the oral cavity and oropharynx of 182 COVID-19 patients compared to 75 unaffected individuals. The samples were obtained from gargle screening samples. 16S rRNA amplicon sequencing was applied to analyze the samples. (3) Results: The present study shows that SARS-CoV-2 infection induced significant differences in bacterial community assemblages, with Prevotella and Veillonella as biomarkers for positive-tested people and Streptococcus and Actinomyces for negative-tested people. It also suggests a state of dysbiosis on the part of the infected individuals due to significant differences in the bacterial community in favor of a microbiome richer in opportunistic pathogens. (4) Conclusions: SARS-CoV-2 infection induces dysbiosis in the upper respiratory tract. The identification of these opportunistic pathogenic biomarkers could be a new screening and prevention tool for people with prior dysbiosis.}, }
@article {pmid38004705, year = {2023}, author = {Mancilla, VJ and Braden-Kuhle, PN and Brice, KN and Mann, AE and Williams, MT and Zhang, Y and Chumley, MJ and Barber, RC and White, SN and Boehm, GW and Allen, MS}, title = {A Synthetic Formula Amino Acid Diet Leads to Microbiome Dysbiosis, Reduced Colon Length, Inflammation, and Altered Locomotor Activity in C57BL/6J Mice.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004705}, issn = {2076-2607}, support = {S21MD012472/MD/NIMHD NIH HHS/United States ; R25GM125587/GM/NIGMS NIH HHS/United States ; }, abstract = {The effects of synthetic, free-amino acid diets, similar to those prescribed as supplements for (phenylketonuria) PKU patients, on gut microbiota and overall health are not well understood. In the current, multidisciplinary study, we examined the effects of a synthetically-derived, low-fiber, amino acid diet on behavior, cognition, gut microbiome composition, and inflammatory markers. A cohort of 20 male C57BL/6J mice were randomly assigned to either a standard or synthetic diet (n = 10) at post-natal day 21 and maintained for 13 weeks. Sequencing of the 16S rRNA gene from fecal samples revealed decreased bacterial diversity, increased abundance of bacteria associated with disease, such as Prevotella, and a downward shift in gut microbiota associated with fermentation pathways in the synthetic diet group. Furthermore, there were decreased levels of short chain fatty acids and shortening of the colon in mice consuming the synthetic diet. Finally, we measured TNF-α, IL-6, and IL-10 in serum, the hippocampus, and colon, and found that the synthetic diet significantly increased IL-6 production in the hippocampus. These results demonstrate the importance of a multidisciplinary approach to future diet and microbiome studies, as diet not only impacts the gut microbiome composition but potentially systemic health as well.}, }
@article {pmid38004678, year = {2023}, author = {Mondal, S and Somani, J and Roy, S and Babu, A and Pandey, AK}, title = {Insect Microbial Symbionts: Ecology, Interactions, and Biological Significance.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004678}, issn = {2076-2607}, support = {BT/PR45283/NER/95/1919/2022//Department of Biotechnology/ ; }, abstract = {The guts of insect pests are typical habitats for microbial colonization and the presence of bacterial species inside the gut confers several potential advantages to the insects. These gut bacteria are located symbiotically inside the digestive tracts of insects and help in food digestion, phytotoxin breakdown, and pesticide detoxification. Different shapes and chemical assets of insect gastrointestinal tracts have a significant impact on the structure and makeup of the microbial population. The number of microbial communities inside the gastrointestinal system differs owing to the varying shape and chemical composition of digestive tracts. Due to their short generation times and rapid evolutionary rates, insect gut bacteria can develop numerous metabolic pathways and can adapt to diverse ecological niches. In addition, despite hindering insecticide management programs, they still have several biotechnological uses, including industrial, clinical, and environmental uses. This review discusses the prevalent bacterial species associated with insect guts, their mode of symbiotic interaction, their role in insecticide resistance, and various other biological significance, along with knowledge gaps and future perspectives. The practical consequences of the gut microbiome and its interaction with the insect host may lead to encountering the mechanisms behind the evolution of pesticide resistance in insects.}, }
@article {pmid38004667, year = {2023}, author = {Kalnina, I and Gudra, D and Silamikelis, I and Viksne, K and Roga, A and Skinderskis, E and Fridmanis, D and Klovins, J}, title = {Variations in the Relative Abundance of Gut Bacteria Correlate with Lipid Profiles in Healthy Adults.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004667}, issn = {2076-2607}, support = {"Investigation of interaction of smoked dietary products with gut microbiota" Agreement Nr. 1.1.1.2/VIAA/1/16/128//European Regional Development Fund "On Implementation of Activity 1.1.1.2 "Post-doctoral Research Aid"/ ; }, abstract = {The gut microbiome is a versatile system regulating numerous aspects of host metabolism. Among other traits, variations in the composition of gut microbial communities are related to blood lipid patterns and hyperlipidaemia, yet inconsistent association patterns exist. This study aims to assess the relationships between the composition of the gut microbiome and variations in lipid profiles among healthy adults. This study used data and samples from 23 adult participants of a previously conducted dietary intervention study. Circulating lipid measurements and whole-metagenome sequences of the gut microbiome were derived from 180 blood and faecal samples collected from eight visits distributed across an 11-week study. Lipid-related variables explained approximately 4.5% of the variation in gut microbiome compositions, with higher effects observed for total cholesterol and high-density lipoproteins. Species from the genera Odoribacter, Anaerostipes, and Parabacteroides correlated with increased serum lipid levels, whereas probiotic species like Akkermansia muciniphila were more abundant among participants with healthier blood lipid profiles. An inverse correlation with serum cholesterol was also observed for Massilistercora timonensis, a player in regulating lipid turnover. The observed correlation patterns add to the growing evidence supporting the role of the gut microbiome as an essential regulator of host lipid metabolism.}, }
@article {pmid38004642, year = {2023}, author = {Smith, ML and Weitz, KK and Thompson, AM and Jansson, JK and Hofmockel, KS and Lipton, MS}, title = {Real-Time and Rapid Respiratory Response of the Soil Microbiome to Moisture Shifts.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004642}, issn = {2076-2607}, abstract = {Microbial response to changing environmental factors influences the fate of soil organic carbon, and drought has been shown to affect microbial metabolism and respiration. We hypothesized that the access of microbes to different carbon pools in response to dry-rewet events occurs sequentially at different rates. We amended desiccated soils with [13]C-labeled glucose and measured the rates of [12]CO2 and [13]CO2 respiration in real time after rewetting. Using these differentiated [12]CO2 and [13]CO2 respiration rate soils after rewetting, we were able to deduce when microbes are accessing different pools of carbon. Immediately upon rewetting, respiration of [12]CO2 occurred first, with negligible [13]CO2 respiration. Appreciable metabolism and respiration of the added [13]C glucose did not occur until 15 min after rewetting. We conclude that, while all carbon pools are being accessed in the first 9 h after rewetting, the rate and timing at which new and existing carbon pools are being accessed varies. Within this study, using stable isotope-labeled substrates to discern which carbon pools are metabolized first uniquely illustrates how microorganisms access different carbon pools which has implications into understanding how carbon metabolism can further affect climate, carbon sequestration, and soil health.}, }
@article {pmid38004641, year = {2023}, author = {Zhao, R and Fajardo, J and Shen, GX}, title = {Influence of Brown or Germinated Brown Rice Supplementation on Fecal Short-Chain Fatty Acids and Microbiome in Diet-Induced Insulin-Resistant Mice.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004641}, issn = {2076-2607}, support = {OG-3-15-4889-GS//Diabetes Canada/ ; }, abstract = {Intake of whole grain foods is associated with improving metabolic profile compared to refined grain products, but the underlying mechanism remains unclear. The present study examined the effects of brown rice (BRR) or germinated brown rice (GBR) supplementation on fecal short-chain fatty acids (SCFAs), and relationship with gut microbiota, metabolism and inflammation in high fat (HF)-diet-fed mice. The results demonstrated that an HF diet supplemented with BRR or GBR comparably increased the abundance of fecal isobutyric acid compared to that in mice receiving HF+white rice (WHR) diet (p < 0.01). The abundance of valeric acid in HF+GBR-diet-fed mice was higher than those receiving HF+WHR diet (p < 0.05). The abundances of fecal isobutyric acid negatively correlated with fasting plasma glucose, insulin, cholesterol, triglycerides, tumor necrosis factor-α, plasminogen activator inhibit-1, monocyte chemotactic protein-1 and homeostatic model assessment of insulin resistance (p < 0.01). The abundance of valeric acids negatively correlated with insulin resistance (p < 0.05). The abundances of isobutyric acid positively correlated with Lactobacillus, but negatively correlated with Dubosiella genus bacteria (p < 0.05). The findings demonstrated that the increases in SCFAs in the feces of BRR and GBR-treated mice were associated with improvements in gut microbiome, metabolic and inflammatory profile, which may contribute to the antidiabetic and anti-inflammatory effects of the whole grains in HF-diet-fed mice.}, }
@article {pmid38004350, year = {2023}, author = {Ren, Y and Ciwang, R and Wang, J and Mehmood, K and Ataya, FS and Li, K}, title = {Effect of Different Feeds on the Fungi Microbiome of Suffolk Crossed with Tibetan Sheep.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, pmid = {38004350}, issn = {2075-1729}, support = {XZ202101ZD0001N//Major projects for the Tibet Autonomous Region/ ; }, abstract = {The gut microbiome plays an important role in the metabolism, nutrient absorption and immunocompetency of animals. The dynamics of the microbiota can be influenced by modulatory factors that involve nutrition, environment, health, diseases, etc. Few reports have been documented regarding the effects of different feeds on the fungi microbiome of Suffolk crossed with Tibetan sheep. A total of 30 Suffolk crossed with Tibetan sheep (ST sheep) were selected for the study and randomly divided into five equal groups (n = 6): AZ, BZ, CZ, DZ and EZ. Group AZ was fed with alfalfa and oat grass, whereas group BZ was fed with mixture of concentrated feed, alfalfa and oat grass. Groups CZ, DZ and EZ were fed with concentrated feed #1, #2 and #3, respectively. All experimental animals were fed twice a day for four months, and rectum samples were collected for microbiota analysis. Results revealed that 2,781,461 raw reads and 2,333,239 clean reads were achieved in the ST sheep. When compared with the sheep of groups AZ and BZ (164), the shared amplicon sequence variants (ASVs) between AZ and CZ (109), AZ (113) and DZ (118) as well as AZ along with EZ were fewer. Conspicuous different phyla (8) and genera (56) were examined and compared with free-range sheep in AZ. Genera including Xeromyces, Kazachstania, Cordyceps, Rhodotorula, Pichia, Spor, etc. were found higher in animals in the CZ, DZ and EZ groups. The results of this study provide new insights regarding the effects of different feeds on the fungi microbiome of sheep farmed on the plateau. We concluded that the differences in feed in Suffolk crossed with Tibetan sheep altered their gut microbiota.}, }
@article {pmid37961388, year = {2023}, 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: Microbial communities of immature Neotropical tick species parasitizing migratory landbirds along northern Gulf of Mexico.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37961388}, support = {P20 GM103476/GM/NIGMS NIH HHS/United States ; }, abstract = {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 lead to the emergence of novel tick-borne pathogens or the re-emergence of previously eradicated ones. This study assessed the prevalence of exotic tick species parasitizing resident, short-distance, and long-distance songbirds during spring and autumn at stopover sites in the northern Gulf of Mexico using the mitochondrial 12S rDNA gene. Birds were captured for tick collection from six different sites from late August to early November in both 2018 and 2019. The highest number of ticks were collected in the 2019 season. Most ticks were collected off the Yellow-breasted Chat (Icteria virens) and Common Yellowthroat (Geothlypis trichas), and 54% of the total ticks collected were from Grand Chenier, LA. A high throughput 16S ribosomal RNA sequencing approach was followed to characterize the microbial communities and identify pathogenic microbes in all tick samples. Tick microbial communities, diversity, and community structure were determined using quantitative insight into microbial ecology (QIIME). The sparse correlations for compositional data (SparCC) approach was then used to construct microbial network maps and infer microbial correlations. A total of 421 individual ticks in the genera Amblyomma, Haemaphysalis, and Ixodes were recorded from 28 songbird species, of which Amblyomma and Amblyomma longirostre was the most abundant tick genus and species, respectively. Microbial profiles showed that Proteobacteria was the most abundant phylum. The most abundant bacteria include the pathogenic Rickettsia and endosymbiont Francisella, Candidatus Midichloria, and Spiroplasma. BLAST analysis and phylogenetic reconstruction of the Rickettsia sequences revealed the highest similarities to pathogenic spotted and non-spotted fever groups, including R. buchneri, R. conorii, R. prowazekii, R. bellii, R. australis, R. parkeri, R. monacensis, and R. monteiroi. Permutation multivariate analysis of variance revealed that the relative abundance of Francisella and Rickettsia drives microbial patterns across the tick genera. We also observed 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 means dispersal distances from 421-5003 kilometers. These findings strongly highlight the potential role of migratory birds in the epidemiology of tick-borne pathogens.}, }
@article {pmid38004243, year = {2023}, author = {Hong, L and Huang, Y and Han, J and Li, S and Zhang, L and Jiang, S and Zhou, Q and Cao, X and Yu, W and Yang, Y and Hong, S and Zhou, Y and Yan, W and Cao, Y}, title = {Dynamics and Crosstalk between Gut Microbiota, Metabolome, and Fecal Calprotectin in Very Preterm Infants: Insights into Feeding Intolerance.}, journal = {Nutrients}, volume = {15}, number = {22}, pages = {}, pmid = {38004243}, issn = {2072-6643}, support = {2021YFC2701800//National Key Research and Development Program of China/ ; 2021YFC2701801//National Key Research and Development Program of China/ ; 2016ZB0101//Key Developing Discipline of the Shanghai Municipal Health Commission (Pediatrics)/ ; }, abstract = {BACKGROUND: Feeding intolerance (FI) is a significant concern in the care of preterm infants, impacting their growth and development. We previously reported that FI is linked to lower fecal calprotectin (FC) levels. This study aims to explore the postnatal dynamics and interplay between microbiota, metabolic profiles, and host immunity in preterm infants with and without FI.<br><br>METHODS: Infants with gestational age <32 weeks or birth weight <1500 g were enrolled at the Children's Hospital of Fudan University between January 2018 and October 2020. Weekly fecal samples were analyzed for bacterial profiling, metabolome, and calprotectin levels, exploring their longitudinal development and interrelationships.<br><br>RESULTS: Of the 118 very preterm infants studied, 48 showed FI. These infants experienced an interrupted microbial-immune trajectory, particularly at 3-4 weeks of age, marked by a reduced bacterial abundance, alpha diversity, and FC levels. Metabolic changes in FI were pronounced between 3 and 6 weeks. Pantothenic acid and two polyamine metabolites were closely associated with bacterial abundance and FC levels and negatively correlated with the duration to attain full enteral feeding.<br><br>CONCLUSIONS: FI infants demonstrated compromised microbiome-immune interactions, potentially influenced by specific metabolites. This research underscored the importance of early microbial and metabolic development in the pathogenesis of FI in very preterm infants.}, }
@article {pmid38004216, year = {2023}, author = {Dębińska, A and Sozańska, B}, title = {Dietary Polyphenols-Natural Bioactive Compounds with Potential for Preventing and Treating Some Allergic Conditions.}, journal = {Nutrients}, volume = {15}, number = {22}, pages = {}, pmid = {38004216}, issn = {2072-6643}, abstract = {In light of the constantly increasing prevalence of allergic diseases, changes in dietary patterns have been suggested as a plausible environmental explanation for the development and progression of these diseases. Nowadays, much attention has been paid to the development of dietary interventions using natural substances with anti-allergy activities. In this respect, dietary polyphenols have been studied extensively as one of the most prominent natural bioactive compounds with well-documented anti-inflammatory, antioxidant, and immunomodulatory properties. This review aims to discuss the mechanisms underlying the potential anti-allergic actions of polyphenols related to their ability to reduce protein allergenicity, regulate immune response, and gut microbiome modification; however, these issues need to be elucidated in detail. This paper reviews the current evidence from experimental and clinical studies confirming that various polyphenols such as quercetin, curcumin, resveratrol, catechins, and many others could attenuate allergic inflammation, alleviate the symptoms of food allergy, asthma, and allergic rhinitis, and prevent the development of allergic immune response. Conclusively, dietary polyphenols are endowed with great anti-allergic potential and therefore could be used either for preventive approaches or therapeutic interventions in relation to allergic diseases. Limitations in studying and widespread use of polyphenols as well as future research directions are also discussed.}, }
@article {pmid38004205, year = {2023}, author = {Lundtorp Olsen, C and Massarenti, L and Vendius, VFD and Gürsoy, UK and Van Splunter, A and Bikker, FJ and Gürsoy, M and Damgaard, C and Markvart, M and Belstrøm, D}, title = {Probiotics Partly Suppress the Impact of Sugar Stress on the Oral Microbiota-A Randomized, Double-Blinded, Placebo-Controlled Trial.}, journal = {Nutrients}, volume = {15}, number = {22}, pages = {}, pmid = {38004205}, issn = {2072-6643}, support = {1044-00093B//Innovation Fund Denmark/ ; Not possible//ADM Denmark A/S/ ; }, abstract = {The aim was to test if probiotics counteract oral dysbiosis during 14 days of sugar stress and subsequently help restore oral homeostasis. Eighty healthy individuals received either probiotics (n = 40) or placebo lozenges (n = 40) for 28 days and rinsed with a 10% sucrose solution 6-8 times during the initial 14 days of the trial. Saliva and supragingival samples were collected at baseline, day 14, and day 28. Saliva samples were analyzed for levels of pro-inflammatory cytokines, albumin, and salivary enzyme activity. The supragingival microbiota was characterized according to the Human Oral Microbiome Database. After 14 days of sugar stress, the relative abundance of Porphyromonas species was significantly higher (p = 0.03) and remained significantly elevated at day 28 in the probiotic group compared to the placebo group (p = 0.004). At day 28, the relative abundance of Kingella species was significantly higher in the probiotic group (p = 0.03). Streptococcus gordinii and Neisseria elongata were associated with the probiotic group on day 28, while Streptococcus sobrinus was associated with the placebo group on day 14 and day 28. On day 28, the salivary albumin level was significantly lower in the probiotic group. The present study demonstrates a potential stabilizing effect on the supragingival microbiota mediated by consumption of probiotics during short-term sugar stress.}, }
@article {pmid38004198, year = {2023}, author = {Suta, S and Ophakas, S and Manosan, T and Honwichit, O and Charoensiddhi, S and Surawit, A and Pongkunakorn, T and Pumeiam, S and Mongkolsucharitkul, P and Pinsawas, B and Sutheeworapong, S and Puangsombat, P and Khoomrung, S and Mayurasakorn, K}, title = {Influence of Prolonged Whole Egg Supplementation on Insulin-like Growth Factor 1 and Short-Chain Fatty Acids Product: Implications for Human Health and Gut Microbiota.}, journal = {Nutrients}, volume = {15}, number = {22}, pages = {}, pmid = {38004198}, issn = {2072-6643}, support = {PRP6105022310, PRP6505030460//Agricultural Research Development Agency/ ; 17108//Mahidol University/ ; }, abstract = {The gut microbiota exert a profound influence on human health and metabolism, with microbial metabolites playing a pivotal role in shaping host physiology. This study investigated the impact of prolonged egg supplementation on insulin-like growth factor 1 (IGF-1) and circulating short-chain fatty acids (SCFAs). In a subset of a cluster-randomized trial, participants aged 8-14 years were randomly assigned into three groups: (1) Whole Egg (WE)-consuming 10 additional eggs per week [n = 24], (2) Protein Substitute (PS)-consuming yolk-free egg substitute equivalent to 10 eggs per week [n = 25], and (3) Control Group (C) [n = 26]. At week 35, IGF-1 levels in WE significantly increased (66.6 ± 27.7 ng/mL, p < 0.05) compared to C, with positive SCFA correlations, except acetate. Acetate was stable in WE, increasing in PS and C. Significant propionate differences occurred between WE and PS (14.8 ± 5.6 μmol/L, p = 0.010). WE exhibited notable changes in the relative abundance of the Bifidobacterium and Prevotella genera. Strong positive SCFA correlations were observed with MAT-CR-H4-C10 and Libanicoccus, while Roseburia, Terrisporobacter, Clostridia_UCG-014, and Coprococcus showed negative correlations. In conclusion, whole egg supplementation improves growth factors that may be related to bone formation and growth; it may also promote benefits to gut microbiota but may not affect SCFAs.}, }
@article {pmid38004180, year = {2023}, author = {Zhou, J and Ho, V}, title = {Role of Baseline Gut Microbiota on Response to Fiber Intervention in Individuals with Irritable Bowel Syndrome.}, journal = {Nutrients}, volume = {15}, number = {22}, pages = {}, pmid = {38004180}, issn = {2072-6643}, support = {Investigator Initiated Funding Scheme//Nestl&#xe9; Foundation/ ; }, abstract = {Irritable bowel syndrome (IBS) is one of the most prevalent functional gut disorders in the world. Partially hydrolyzed guar gum, a low-viscosity soluble fiber, has shown promise in the management of IBS-related symptoms. In this study, we aimed to determine if an individual's baseline gut microbiota impacted their response to a partially hydrolyzed guar gum intervention. Patients diagnosed with IBS undertook a 90-day intervention and follow-up. IBS symptom severity, tolerability, quality-of-life, and fecal microbiome composition were recorded during this study. Patients with normal microbiota diversity (Shannon index ≥ 3) showed significant improvements to IBS symptom scores, quality-of-life, and better tolerated the intervention compared to patients with low microbiota diversity (Shannon index < 3). Our findings suggest that an individual's baseline microbiome composition exerts a substantial influence on their response to fiber intervention. Future investigations should explore a symbiotic approach to the treatment of IBS.}, }
@article {pmid38004139, year = {2023}, author = {Song, S and Shon, J and Yang, WR and Kang, HB and Kim, KH and Park, JY and Lee, S and Baik, SY and Lee, KR and Park, YJ}, title = {Short-Term Effects of Weight-Loss Meal Replacement Programs with Various Macronutrient Distributions on Gut Microbiome and Metabolic Parameters: A Pilot Study.}, journal = {Nutrients}, volume = {15}, number = {22}, pages = {}, pmid = {38004139}, issn = {2072-6643}, support = {2021R1A2C2012578//National Research Foundation of Korea/ ; }, abstract = {It has emerged the gut microbiome is crucially linked to metabolic health and obesity. Macronutrient distribution has been discussed as a key parameter in weight-loss programs, but little is known about its impact on the gut microbiome. We investigated the effects of weight-loss meal replacement programs with different macronutrient ratios on the gut microbiota and metabolic parameters in subjects with overweight and obesity. Three low-calorie meal replacement programs with different ratios of carbohydrates, proteins, and lipids were designed: a balanced diet (Group B, 60:15:30), a high-lipid-low-carbohydrate diet (Group F, 35:20:55), and a protein-enriched diet (Group P, 40:25:35). Sixty overweight or obese participants were provided with the meals twice daily for 3 weeks. In all groups, diet intervention resulted in reduced body weight and BMI. The relative abundance of Bacteroidetes and Firmicutes phyla decreased and increased, respectively, which increased the Firmicutes/Bacteroidetes (F/B) ratio in all subjects, particularly in Groups B and P. Alpha- and beta-diversity were augmented at the phylum level in Group P. In conclusion, short-term interventions with weight-loss meal replacement programs increased butyrate-producing bacteria and the F/B ratio. Moreover, the protein-enriched diet significantly increased alpha- and beta-diversity compared to the balanced diet and the high-lipid-low-carbohydrate diet.}, }
@article {pmid38004133, year = {2023}, author = {Wang, C and Zhu, H and Cheng, Y and Guo, Y and Zhao, Y and Qian, H}, title = {Aqueous Extract of Brassica rapa L.'s Impact on Modulating Exercise-Induced Fatigue via Gut-Muscle Axis.}, journal = {Nutrients}, volume = {15}, number = {22}, pages = {}, pmid = {38004133}, issn = {2072-6643}, support = {Nos. 2020YFC1606800//The Wuxi Taihu Lake Talent Plan, National Key Research and Development Program of China/ ; 2022YFF1101103//The National Key Research and Development Program of China/ ; Q202150//The Youth Talent Project of Wuxi Health Commission/ ; }, abstract = {Exercise-induced fatigue is a common physiological response to prolonged physical activity, often associated with changes in gut microbiota and metabolic responses. This study investigates the potential role of Brassica rapa L. in modulating these responses. Using an animal model subjected to chronic exercise-induced stress, we explored the effects of Brassica rapa L. on fatigue-related biomarkers, energy metabolism genes, inflammatory responses, intestinal integrity, and gut microbiota composition. Our findings revealed that Brassica rapa L. exhibits significant antioxidant activity and effectively modulates physiological responses to fatigue. It influences gene expression related to the tricarboxylic acid (TCA) cycle in muscle tissue through the AMPK/PGC-1α/TFAM signaling pathway. Furthermore, Brassica rapa L. has been found to alleviate inflammation by inhibiting lipopolysaccharide (LPS) infection and suppressing the activation of the NF-κB pathway. It also maintains intestinal integrity and controls Gram-negative bacterial growth. A correlation analysis identified several pathogenic bacteria linked with inflammation and energy metabolism, as well as beneficial probiotic bacteria associated with improved energy metabolism and reduced inflammation. These findings underscore Brassica rapa L.'s potential for managing prolonged exercise-induced fatigue, paving the way for future therapeutic applications. The results highlight its impact on gut microbiota modulation and its role in nutrition science and sports medicine.}, }
@article {pmid38004131, year = {2023}, author = {Gao, X and Yin, P and Ren, Y and Yu, L and Tian, F and Zhao, J and Chen, W and Xue, Y and Zhai, Q}, title = {Predicting Personalized Diets Based on Microbial Characteristics between Patients with Superficial Gastritis and Atrophic Gastritis.}, journal = {Nutrients}, volume = {15}, number = {22}, pages = {}, pmid = {38004131}, issn = {2072-6643}, support = {32122067//National Natural Science Foundation of China/ ; 32021005//National Natural Science Foundation of China/ ; BK20200084//Natural Science Foundation of Jiangsu Province/ ; ZDRC039//Key Talents Project of "Strengthening Health through Science and Education" of Wuxi Health and Family Planning Commission/ ; LGY2018016//Top Talents Project of "Six-one Project" for High-level Health Talents in Jiangsu Province/ ; }, abstract = {BACKGROUND: gastritis is a common stomach disease with a high global incidence and can potentially develop into gastric cancer. The treatment of gastritis focuses on medication or diets based on national guidelines. However, the specific diet that can alleviate gastritis remains largely unknown.<br><br>METHODS: we propose a microbiota-directed dietary strategy that investigates potential food factors using microbial exogenous metabolites. Given the current lack of understanding of the repeatable characteristics of gastric microbiota, we conducted a meta-analysis to identify the features of gastric bacteria. Local samples were collected as validation cohorts. Furthermore, RevEcoR was employed to identify bacteria's exogenous metabolites, and FooDB was used to retrieve foods that can target specific bacteria.<br><br>RESULTS: Bacteroides, Weissella, Actinomyces, Atopobium, Oribacterium, Peptostreptococcus, and Rothia were biomarkers between superficial gastritis (SG) and atrophic gastritis (AG) (AG_N) without H. pylori infection, whereas Bacillus, Actinomyces, Cutibacterium, Helicobacter, Novosphingobium, Pseudomonas, and Streptococcus were signatures between SG and AG (AG_P) with H. pylori infection. According to the exogenous metabolites, adenosyloobalamin, soybean, common wheat, dates, and barley were regarded as potential candidates for AG_N treatment, while gallate was regarded as a candidate for AG_P treatment.<br><br>CONCLUSIONS: this study firstly profiled the gastric microbiota of AG and SG with or without H. pylori and provided a recommended diet for global AG according to exogenous metabolites.}, }
@article {pmid38004128, year = {2023}, author = {He, S and Lin, F and Hu, X and Pan, P}, title = {Gut Microbiome-Based Therapeutics in Critically Ill Adult Patients-A Narrative Review.}, journal = {Nutrients}, volume = {15}, number = {22}, pages = {}, pmid = {38004128}, issn = {2072-6643}, support = {z047-02//The national key clinical specialist construction programs of China/ ; }, abstract = {The gut microbiota plays a crucial role in the human microenvironment. Dysbiosis of the gut microbiota is a common pathophysiological phenomenon in critically ill patients. Therefore, utilizing intestinal microbiota to prevent complications and improve the prognosis of critically ill patients is a possible therapeutic direction. The gut microbiome-based therapeutics approach focuses on improving intestinal microbiota homeostasis by modulating its diversity, or treating critical illness by altering the metabolites of intestinal microbiota. There is growing evidence that fecal microbiota transplantation (FMT), selective digestive decontamination (SDD), and microbiota-derived therapies are all effective treatments for critical illness. However, different treatments are appropriate for different conditions, and more evidence is needed to support the selection of optimal gut microbiota-related treatments for different diseases. This narrative review summarizes the curative effects and limitations of microbiome-based therapeutics in different critically ill adult patients, aiming to provide possible directions for gut microbiome-based therapeutics for critically ill patients such as ventilator-associated pneumonia, sepsis, acute respiratory distress syndrome, and COVID-19, etc.}, }
@article {pmid38004098, year = {2023}, author = {López-Montoya, P and Rivera-Paredez, B and Palacios-González, B and Morán-Ramos, S and López-Contreras, BE and Canizales-Quinteros, S and Salmerón, J and Velázquez-Cruz, R}, title = {Dietary Patterns Are Associated with the Gut Microbiome and Metabolic Syndrome in Mexican Postmenopausal Women.}, journal = {Nutrients}, volume = {15}, number = {22}, pages = {}, pmid = {38004098}, issn = {2072-6643}, support = {Grant numbers: 7876, 87783, 262233, 26267M, SALUD-2010-01-139796, SALUD-2011-01-161930, and CB-2013-01-221628//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; Proyecto FPIS2023-INMEGEN-5251//"Financiamiento de Proyectos de Investigaci&#xf3;n para la Salud" (FPIS) 2023/ ; }, abstract = {Postmenopausal women are at an increased risk of developing metabolic syndrome (MetS) due to hormonal changes and lifestyle factors. Gut microbiota (GM) have been linked to the development of MetS, and they are influenced by dietary habits. However, the interactions between dietary patterns (DP) and the GM of postmenopausal women, as well as their influence on MetS, still need to be understood. The present study evaluated the DP and microbiota composition of postmenopausal Mexican women with MetS and those in a control group. Diet was assessed using a food frequency questionnaire, and the GM were profiled using 16S rRNA gene sequencing. Greater adherence to a "healthy" DP was significantly associated with lower values of MetS risk factors. GM diversity was diminished in women with MetS, and it was negatively influenced by an "unhealthy" DP. Moreover, a higher intake of fats and proteins, as well as lower amounts of carbohydrates, showed a reduction in some of the short-chain fatty acid-producing genera in women with MetS, as well as increases in some harmful bacteria. Furthermore, Roseburia abundance was positively associated with dietary fat and waist circumference, which may explain 7.5% of the relationship between this macronutrient and MetS risk factors. These findings suggest that GM and diet interactions are important in the development of MetS in postmenopausal Mexican women.}, }
@article {pmid38004014, year = {2023}, author = {Biţă, CE and Scorei, IR and Vreju, AF and Muşetescu, AE and Mogoşanu, GD and Biţă, A and Dinescu, VC and Dinescu, &#x15e;C and Criveanu, C and Bărbulescu, AL and Florescu, A and Ciurea, PL}, title = {Microbiota-Accessible Boron-Containing Compounds in Complex Regional Pain Syndrome.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {59}, number = {11}, pages = {}, pmid = {38004014}, issn = {1648-9144}, support = {POCU/993/6/13/153178//European Social Fund within the Sectorial Operational Program Human Capital 2014-2020/ ; }, abstract = {The microbiota-gut-brain axis has garnered increasing attention in recent years for its role in various health conditions, including neuroinflammatory disorders like complex regional pain syndrome (CRPS). CRPS is a debilitating condition characterized by chronic neuropathic pain, and its etiology and pathophysiology remain elusive. Emerging research suggests that alterations in the gut microbiota composition and function could play a significant role in CRPS development and progression. Our paper explores the implications of microbiota in CRPS and the potential therapeutic role of boron (B). Studies have demonstrated that individuals with CRPS often exhibit dysbiosis, with imbalances in beneficial and pathogenic gut bacteria. Dysbiosis can lead to increased gut permeability and systemic inflammation, contributing to the chronic pain experienced in CRPS. B, an essential trace element, has shown promise in modulating the gut microbiome positively and exerting anti-inflammatory effects. Recent preclinical and clinical studies suggest that B supplementation may alleviate neuropathic pain and improve CRPS symptoms by restoring microbiota balance and reducing inflammation. Our review highlights the complex interplay between microbiota, inflammation, and neuropathic pain in CRPS and underscores the potential of B as a novel therapeutic approach to target the microbiota-gut-brain axis, offering hope for improved management of this challenging condition.}, }
@article {pmid38003917, year = {2023}, author = {Ispas, S and Tuta, LA and Botnarciuc, M and Ispas, V and Staicovici, S and Ali, S and Nelson-Twakor, A and Cojocaru, C and Herlo, A and Petcu, A}, title = {Metabolic Disorders, the Microbiome as an Endocrine Organ, and Their Relations with Obesity: A Literature Review.}, journal = {Journal of personalized medicine}, volume = {13}, number = {11}, pages = {}, pmid = {38003917}, issn = {2075-4426}, abstract = {UNLABELLED: The etiology of metabolic disorders, such as obesity, has been predominantly associated with the gut microbiota, which is acknowledged as an endocrine organ that plays a crucial role in modulating energy homeostasis and host immune responses. The presence of dysbiosis has the potential to impact the functioning of the intestinal barrier and the gut-associated lymphoid tissues by allowing the transit of bacterial structural components, such as lipopolysaccharides. This, in turn, may trigger inflammatory pathways and potentially lead to the onset of insulin resistance. Moreover, intestinal dysbiosis has the potential to modify the production of gastrointestinal peptides that are linked to the feeling of fullness, hence potentially leading to an increase in food consumption. In this literature review, we discuss current developments, such as the impact of the microbiota on lipid metabolism as well as the processes by which its changes led to the development of metabolic disorders. Several methods have been developed that could be used to modify the gut microbiota and undo metabolic abnormalities.<br><br>METHODS: After researching different databases, we examined the PubMed collection of articles and conducted a literature review.<br><br>RESULTS: After applying our exclusion and inclusion criteria, the initial search yielded 1345 articles. We further used various filters to narrow down our titles analysis and, to be specific to our study, selected the final ten studies, the results of which are included in the Results section.<br><br>CONCLUSIONS: Through gut barrier integrity, insulin resistance, and other influencing factors, the gut microbiota impacts the host's metabolism and obesity. Although the area of the gut microbiota and its relationship to obesity is still in its initial stages of research, it offers great promise for developing new therapeutic targets that may help prevent and cure obesity by restoring the gut microbiota to a healthy condition.}, }
@article {pmid38003905, year = {2023}, author = {Fawaz, A and Ferraresi, A and Isidoro, C}, title = {Systems Biology in Cancer Diagnosis Integrating Omics Technologies and Artificial Intelligence to Support Physician Decision Making.}, journal = {Journal of personalized medicine}, volume = {13}, number = {11}, pages = {}, pmid = {38003905}, issn = {2075-4426}, abstract = {Cancer is the second major cause of disease-related death worldwide, and its accurate early diagnosis and therapeutic intervention are fundamental for saving the patient's life. Cancer, as a complex and heterogeneous disorder, results from the disruption and alteration of a wide variety of biological entities, including genes, proteins, mRNAs, miRNAs, and metabolites, that eventually emerge as clinical symptoms. Traditionally, diagnosis is based on clinical examination, blood tests for biomarkers, the histopathology of a biopsy, and imaging (MRI, CT, PET, and US). Additionally, omics biotechnologies help to further characterize the genome, metabolome, microbiome traits of the patient that could have an impact on the prognosis and patient's response to the therapy. The integration of all these data relies on gathering of several experts and may require considerable time, and, unfortunately, it is not without the risk of error in the interpretation and therefore in the decision. Systems biology algorithms exploit Artificial Intelligence (AI) combined with omics technologies to perform a rapid and accurate analysis and integration of patient's big data, and support the physician in making diagnosis and tailoring the most appropriate therapeutic intervention. However, AI is not free from possible diagnostic and prognostic errors in the interpretation of images or biochemical-clinical data. Here, we first describe the methods used by systems biology for combining AI with omics and then discuss the potential, challenges, limitations, and critical issues in using AI in cancer research.}, }
@article {pmid38003898, year = {2023}, author = {Loperfido, A and Cavaliere, C and Begvarfaj, E and Ciofalo, A and D'Erme, G and De Vincentiis, M and Greco, A and Millarelli, S and Bellocchi, G and Masieri, S}, title = {The Impact of Antibiotics and Steroids on the Nasal Microbiome in Patients with Chronic Rhinosinusitis: A Systematic Review According to PICO Criteria.}, journal = {Journal of personalized medicine}, volume = {13}, number = {11}, pages = {}, pmid = {38003898}, issn = {2075-4426}, abstract = {BACKGROUND: The nasal microbiome represents the main environmental factor of the inflammatory process in chronic rhinosinusitis (CRS). Antibiotics and steroids constitute the mainstay of CRS therapies. However, their impact on microbial communities needs to be better understood. This systematic review summarizes the evidence about antibiotics' and steroids' impact on the nasal microbiota in patients with CRS.<br><br>METHODS: The search strategy was conducted in accordance with the PRISMA guidelines for systematic reviews. The authors searched all papers in the three major medical databases (PubMed, Scopus, and Cochrane Library) using the PICO tool (population, intervention, comparison, and outcomes). The search was carried out using a combination of the key terms "Microbiota" or "Microbiome" and "Chronic Rhinosinusitis".<br><br>RESULTS: Overall, 402 papers were identified, and after duplicate removal (127 papers), excluding papers off-topic (154) and for other structural reasons (110), papers were assessed for eligibility; finally, only 11 papers were included and summarized in the present systematic review. Some authors used only steroids, other researchers used only antibiotics, and others used both antibiotics and steroids. With regard to the use of steroids as exclusive medical treatment, topical mometasone and budesonide were investigated. With regard to the use of antibiotics as exclusive medical treatments, clarithromycin, doxycycline, roxithromycin, and amoxicillin clavulanate were investigated. Regarding the use of both antibiotics and steroids, two associations were investigated: systemic prednisone combined with amoxicillin clavulanate and topical budesonide combined with azithromycin.<br><br>CONCLUSIONS: The impact that therapies can have on the nasal microbiome of CRS patients is very varied. Further studies are needed to understand the role of the nasal microbiome, prevent CRS, and improve therapeutic tools for personalized medicine tailored to the individual patient.}, }
@article {pmid38003804, year = {2023}, author = {Alsholi, DM and Yacoub, GS and Rehman, AU and Ullah, H and Khan, AI and Deng, T and Siddiqui, NZ and Alioui, Y and Farooqui, NA and Elkharti, M and Li, Y and Wang, L and Xin, Y}, title = {Lactobacillus rhamnosus Attenuates Cisplatin-Induced Intestinal Mucositis in Mice via Modulating the Gut Microbiota and Improving Intestinal Inflammation.}, journal = {Pathogens (Basel, Switzerland)}, volume = {12}, number = {11}, pages = {}, pmid = {38003804}, issn = {2076-0817}, support = {2019GBJ011630//Chinese Scholarship Council grant number/ ; 31600614, 82072953//the National Nature Science Foundation of China/ ; 2023JJ12SN029//Dalian Science and Technology Innovation Fund Application Foundation Project/ ; 2021-MS-287//Liaoning Natural Science Foundation Program/ ; 2021RJ12//Dalian outstanding young scientific and technological talents/ ; }, abstract = {Lactobacillus rhamnosus (LBS) is a well-documented probiotic strain in oncology and has a pivotal role in clinical applications. Here, we have investigated the protective effect of Lactobacillus rhamnosus on intestinal mucositis induced by cisplatin (CP) and explored the underlying mechanisms targeting inflammatory proteins, as well as the histological changes in the intestinal tissue of mice, in addition, the bacterial strains that may be related to the health-enhancing properties. BALB/c mice were pre-treated with or without LBS via oral gavage, followed by mucositis induction with cisplatin. Our results revealed that the LBS-treated groups significantly attenuated proinflammatory cytokine levels (IL-1β, IL-6, and TNF-α) compared to the CP group. Furthermore, LBS mitigated the damaged tight junction integrity caused by CP via up-regulating the levels of claudin, occludin, ZO-1, and mucin-2 protein (MUC-2). Finally, the 16S rRNA fecal microbiome genomic analysis showed that LBS administration enhanced the growth of beneficial bacteria, i.e., Firmicutes and Lachnospiraceae, while the relative abundance of the opportunistic bacteria Bacteroides and Proteobacteria decreased. Collectively, LBS was found to beneficially modulate microbial composition structure and functions and enrich the ecological diversity in the gut.}, }
@article {pmid38003787, year = {2023}, author = {Thompson, MEH and Shrestha, A and Rinne, J and Limay-Rios, V and Reid, L and Raizada, MN}, title = {The Cultured Microbiome of Pollinated Maize Silks Shifts after Infection with Fusarium graminearum and Varies by Distance from the Site of Pathogen Inoculation.}, journal = {Pathogens (Basel, Switzerland)}, volume = {12}, number = {11}, pages = {}, pmid = {38003787}, issn = {2076-0817}, support = {054810//Grain Farmers of Ontario/ ; 030356, 030564//Ministry of Agriculture, Food and Rural Affairs/ ; 401424, 401663, 400924//Natural Sciences and Engineering Research Council/ ; }, abstract = {Styles transmit pollen-derived sperm nuclei from pollen to ovules, but also transmit environmental pathogens. The microbiomes of styles are likely important for reproduction/disease, yet few studies exist. Whether style microbiome compositions are spatially responsive to pathogens is unknown. The maize pathogen Fusarium graminearum enters developing grain through the style (silk). We hypothesized that F. graminearum treatment shifts the cultured transmitting silk microbiome (TSM) compared to healthy silks in a distance-dependent manner. Another objective of the study was to culture microbes for future application. Bacteria were cultured from husk-covered silks of 14 F. graminearum-treated diverse maize genotypes, proximal (tip) and distal (base) to the F. graminearum inoculation site. Long-read 16S sequences from 398 isolates spanned 35 genera, 71 species, and 238 OTUs. More bacteria were cultured from F. graminearum-inoculated tips (271 isolates) versus base (127 isolates); healthy silks were balanced. F. graminearum caused a collapse in diversity of ~20-25% across multiple taxonomic levels. Some species were cultured exclusively or, more often, from F. graminearum-treated silks (e.g., Delftia acidovorans, Klebsiella aerogenes, K. grimontii, Pantoea ananatis, Stenotrophomonas pavanii). Overall, the results suggest that F. graminearum alters the TSM in a distance-dependent manner. Many isolates matched taxa that were previously identified using V4-MiSeq (core and F. graminearum-induced), but long-read sequencing clarified the taxonomy and uncovered greater diversity than was initially predicted (e.g., within Pantoea). These isolates represent the first comprehensive cultured collection from pathogen-treated maize silks to facilitate biocontrol efforts and microbial marker-assisted breeding.}, }
@article {pmid38003760, year = {2023}, author = {Soldati, KR and Jiang, Y and Brandt, BW and Exterkate, RAM and Buijs, MJ and Nazmi, K and Kaman, WE and Cheng, L and Bikker, FJ and Crielaard, W and Zandim-Barcelos, DL and Deng, DM}, title = {Differential Modulation of Saliva-Derived Microcosm Biofilms by Antimicrobial Peptide LL-31 and D-LL-31.}, journal = {Pathogens (Basel, Switzerland)}, volume = {12}, number = {11}, pages = {}, pmid = {38003760}, issn = {2076-0817}, abstract = {Microbiome modulation, aiming to restore a health-compatible microbiota, is a novel strategy to treat periodontitis. This study evaluated the modulation effects of antimicrobial peptide LL-31 and its D-enantiomer (D-LL-31) on saliva-derived microcosm biofilms, spiked with or without Porphyromonas gingivalis. To this end, one-day-old biofilms were incubated for 24 h with biofilm medium alone, or medium containing 40 µM LL-31 or D-LL-31, after which biofilms were grown for 5 days. Biofilms were assessed at 1 day and 5 days after intervention for the total viable cell counts, dipeptidyl peptidase IV (DPP4) activity, P. gingivalis amount (by qPCR) and microbial composition (by sequencing). The results showed that D-LL-31, not LL-31, significantly reduced the total viable cell counts, the P. gingivalis amount, and the DPP4 activity of the biofilms spiked with P. gingivalis, but only at 1 day after intervention. In the biofilms spiked with P. gingivalis, D-LL-31 tended to reduce the α-diversity and the compositional shift of the biofilms in time as compared to the control and LL-31 groups. In conclusion, D-LL-31 showed a better performance than LL-31 in biofilm modulation. The biofilm modulation function of the peptides could be impaired when the biofilms were in a severely dysbiotic state.}, }
@article {pmid38003752, year = {2023}, author = {Garrigós, M and Garrido, M and Panisse, G and Veiga, J and Martínez-de la Puente, J}, title = {Interactions between West Nile Virus and the Microbiota of Culex pipiens Vectors: A Literature Review.}, journal = {Pathogens (Basel, Switzerland)}, volume = {12}, number = {11}, pages = {}, pmid = {38003752}, issn = {2076-0817}, support = {PID2020-118205GB-I00//Ministerio Espa&#xf1;ol de Ciencia e Innovaci&#xf3;n/ ; PRE2021-098544//Ministerio Espa&#xf1;ol de Ciencia e Innovaci&#xf3;n/ ; FJC2021-048057-I//Ministerio Espa&#xf1;ol de Ciencia e Innovaci&#xf3;n/ ; Mar&#xed;a Zambrano//Ministerio Espa&#xf1;ol de Universidades/ ; Margarita Salas//Ministerio Espa&#xf1;ol de Universidades/ ; P21_00049//Junta de Andaluc&#xed;a, Consejer&#xed;a de Universidad, Investigaci&#xf3;n e Innovaci&#xf3;n/ ; }, abstract = {The flavivirus West Nile virus (WNV) naturally circulates between mosquitoes and birds, potentially affecting humans and horses. Different species of mosquitoes play a role as vectors of WNV, with those of the Culex pipiens complex being particularly crucial for its circulation. Different biotic and abiotic factors determine the capacity of mosquitoes for pathogen transmission, with the mosquito gut microbiota being recognized as an important one. Here, we review the published studies on the interactions between the microbiota of the Culex pipiens complex and WNV infections in mosquitoes. Most articles published so far studied the interactions between bacteria of the genus Wolbachia and WNV infections, obtaining variable results regarding the directionality of this relationship. In contrast, only a few studies investigate the role of the whole microbiome or other bacterial taxa in WNV infections. These studies suggest that bacteria of the genera Serratia and Enterobacter may enhance WNV development. Thus, due to the relevance of WNV in human and animal health and the important role of mosquitoes of the Cx. pipiens complex in its transmission, more research is needed to unravel the role of mosquito microbiota and those factors affecting this microbiota on pathogen epidemiology. In this respect, we finally propose future lines of research lines on this topic.}, }
@article {pmid38003692, year = {2023}, author = {Maslennikov, R and Poluektova, E and Zolnikova, O and Sedova, A and Kurbatova, A and Shulpekova, Y and Dzhakhaya, N and Kardasheva, S and Nadinskaia, M and Bueverova, E and Nechaev, V and Karchevskaya, A and Ivashkin, V}, title = {Gut Microbiota and Bacterial Translocation in the Pathogenesis of Liver Fibrosis.}, journal = {International journal of molecular sciences}, volume = {24}, number = {22}, pages = {}, doi = {10.3390/ijms242216502}, pmid = {38003692}, issn = {1422-0067}, abstract = {Cirrhosis is the end result of liver fibrosis in chronic liver diseases. Studying the mechanisms of its development and developing measures to slow down and regress it based on this knowledge seem to be important tasks for medicine. Currently, disorders of the gut-liver axis have great importance in the pathogenesis of cirrhosis. However, gut dysbiosis, which manifests as increased proportions in the gut microbiota of Bacilli and Proteobacteria that are capable of bacterial translocation and a decreased proportion of Clostridia that strengthen the intestinal barrier, occurs even at the pre-cirrhotic stage of chronic liver disease. This leads to the development of bacterial translocation, a process by which those microbes enter the blood of the portal vein and then the liver tissue, where they activate Kupffer cells through Toll-like receptor 4. In response, the Kupffer cells produce profibrogenic cytokines, which activate hepatic stellate cells, stimulating their transformation into myofibroblasts that produce collagen and other elements of the extracellular matrix. Blocking bacterial translocation with antibiotics, probiotics, synbiotics, and other methods could slow down the progression of liver fibrosis. This was shown in a number of animal models but requires further verification in long-term randomized controlled trials with humans.}, }
@article {pmid38003647, year = {2023}, author = {Angelova, IY and Kovtun, AS and Averina, OV and Koshenko, TA and Danilenko, VN}, title = {Unveiling the Connection between Microbiota and Depressive Disorder through Machine Learning.}, journal = {International journal of molecular sciences}, volume = {24}, number = {22}, pages = {}, doi = {10.3390/ijms242216459}, pmid = {38003647}, issn = {1422-0067}, support = {20-14-00132//Russian Science Foundation/ ; }, abstract = {In the last few years, investigation of the gut-brain axis and the connection between the gut microbiota and the human nervous system and mental health has become one of the most popular topics. Correlations between the taxonomic and functional changes in gut microbiota and major depressive disorder have been shown in several studies. Machine learning provides a promising approach to analyze large-scale metagenomic data and identify biomarkers associated with depression. In this work, machine learning algorithms, such as random forest, elastic net, and You Only Look Once (YOLO), were utilized to detect significant features in microbiome samples and classify individuals based on their disorder status. The analysis was conducted on metagenomic data obtained during the study of gut microbiota of healthy people and patients with major depressive disorder. The YOLO method showed the greatest effectiveness in the analysis of the metagenomic samples and confirmed the experimental results on the critical importance of a reduction in the amount of Faecalibacterium prausnitzii for the manifestation of depression. These findings could contribute to a better understanding of the role of the gut microbiota in major depressive disorder and potentially lead the way for novel diagnostic and therapeutic strategies.}, }
@article {pmid38003531, year = {2023}, author = {Šešelja, K and Bazina, I and Vrecl, M and Farger, J and Schicht, M and Paulsen, F and Baus Lončar, M and Pirman, T}, title = {Tff3 Deficiency Differentially Affects the Morphology of Male and Female Intestines in a Long-Term High-Fat-Diet-Fed Mouse Model.}, journal = {International journal of molecular sciences}, volume = {24}, number = {22}, pages = {}, doi = {10.3390/ijms242216342}, pmid = {38003531}, issn = {1422-0067}, support = {IP-06-2016-2717//Croatian Science Foundation/ ; 2014-2020//European Structural Found (financial support for Ph.D student)/ ; German project No. 57448642//Bilateral Croatian -Germany project of student exchange/ ; P4-0097//Slovenian Research Agency/ ; P4-0053//Slovenian Research Agency/ ; }, abstract = {Trefoil factor family protein 3 (Tff3) protects the gastrointestinal mucosa and has a complex mode of action in different tissues. Here, we aimed to determine the effect of Tff3 deficiency on intestinal tissues in a long-term high-fat-diet (HFD)-fed model. A novel congenic strain without additional metabolically relevant mutations (Tff3-/-/C57Bl6NCrl strain, male and female) was used. Wild type (Wt) and Tff3-deficient mice of both sexes were fed a HFD for 36 weeks. Long-term feeding of a HFD induces different effects on the intestinal structure of Tff3-deficient male and female mice. For the first time, we found sex-specific differences in duodenal morphology. HFD feeding reduced microvilli height in Tff3-deficient females compared to that in Wt females, suggesting a possible effect on microvillar actin filament dynamics. These changes could not be attributed to genes involved in ER and oxidative stress, apoptosis, or inflammation. Tff3-deficient males exhibited a reduced cecal crypt depth compared to that of Wt males, but this was not the case in females. Microbiome-related short-chain fatty acid content was not affected by Tff3 deficiency in HFD-fed male or female mice. Sex-related differences due to Tff3 deficiency imply the need to consider both sexes in future studies on the role of Tff in intestinal function.}, }
@article {pmid38003489, year = {2023}, author = {Pai, AH and Wang, YW and Lu, PC and Wu, HM and Xu, JL and Huang, HY}, title = {Gut Microbiome-Estrobolome Profile in Reproductive-Age Women with Endometriosis.}, journal = {International journal of molecular sciences}, volume = {24}, number = {22}, pages = {}, doi = {10.3390/ijms242216301}, pmid = {38003489}, issn = {1422-0067}, support = {CMRPG3G1981, CMRPG3K0782//Linkou Chang Gung Memorial Hospital/ ; }, abstract = {Microbiota is associated with our bodily functions and microenvironment. A healthy, balanced gut microbiome not only helps maintain mucosal integrity, prevents translocation of bacterial content, and contributes to immune status, but also associates with estrogen metabolism. Gut dysbiosis and estrobolome dysfunction have hence been linked to certain estrogen-dependent diseases, including endometriosis. While prior studies on microbiomes and endometriosis have shown conflicting results, most of the observed microbial differences are seen in the genital tract. This case-control study of reproductive-age women utilizes their fecal and urine samples for enzymatic, microbial, and metabolic studies to explore if patients with endometriosis have distinguishable gut microbiota or altered estrogen metabolism. While gut β-glucuronidase activities, microbial diversity, and abundance did not vary significantly between patients with or without endometriosis, fecal samples of patients with endometriosis were more enriched by the Erysipelotrichia class and had higher folds of four estrogen/estrogen metabolites. Further studies are needed to elucidate what these results imply and whether there indeed is an association or causation between gut microbiota and endometriosis.}, }
@article {pmid38003359, year = {2023}, author = {Siebieszuk, A and Sejbuk, M and Witkowska, AM}, title = {Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping.}, journal = {International journal of molecular sciences}, volume = {24}, number = {22}, pages = {}, doi = {10.3390/ijms242216169}, pmid = {38003359}, issn = {1422-0067}, abstract = {The recently observed circadian oscillations of the intestinal microbiota underscore the profound nature of the human-microbiome relationship and its importance for health. Together with the discovery of circadian clocks in non-photosynthetic gut bacteria and circadian rhythms in anucleated cells, these findings have indicated the possibility that virtually all microorganisms may possess functional biological clocks. However, they have also raised many essential questions concerning the fundamentals of biological timekeeping, its evolution, and its origin. This narrative review provides a comprehensive overview of the recent literature in molecular chronobiology, aiming to bring together the latest evidence on the structure and mechanisms driving microbial biological clocks while pointing to potential applications of this knowledge in medicine. Moreover, it discusses the latest hypotheses regarding the evolution of timing mechanisms and describes the functions of peroxiredoxins in cells and their contribution to the cellular clockwork. The diversity of biological clocks among various human-associated microorganisms and the role of transcriptional and post-translational timekeeping mechanisms are also addressed. Finally, recent evidence on metabolic oscillators and host-microbiome communication is presented.}, }
@article {pmid38003317, year = {2023}, author = {Liu, L and Mahalak, KK and Bobokalonov, JT and Narrowe, AB and Firrman, J and Lemons, JMS and Bittinger, K and Hu, W and Jones, SM and Moustafa, AM}, title = {Impact of Ivermectin on the Gut Microbial Ecosystem.}, journal = {International journal of molecular sciences}, volume = {24}, number = {22}, pages = {}, doi = {10.3390/ijms242216125}, pmid = {38003317}, issn = {1422-0067}, support = {In-House Project 8072-41000-108-00-D//United States Department of Agriculture/ ; }, abstract = {Ivermectin is a an anti-helminthic that is critical globally for both human and veterinary care. To the best of our knowledge, information available regarding the influence of ivermectin (IVM) on the gut microbiota has only been collected from diseased donors, who were treated with IVM alone or in combination with other medicines. Results thus obtained were influenced by multiple elements beyond IVM, such as disease, and other medical treatments. The research presented here investigated the impact of IVM on the gut microbial structure established in a Triple-SHIME[®] (simulator of the human intestinal microbial ecosystem), using fecal material from three healthy adults. The microbial communities were grown using three different culture media: standard SHIME media and SHIME media with either soluble or insoluble fiber added (control, SF, ISF). IVM introduced minor and temporary changes to the gut microbial community in terms of composition and metabolite production, as revealed by 16S rRNA amplicon sequencing analysis, flow cytometry, and GC-MS. Thus, it was concluded that IVM is not expected to induce dysbiosis or yield adverse effects if administered to healthy adults. In addition, the donor's starting community influences the relationship between IVM and the gut microbiome, and the soluble fiber component in feed could protect the gut microbiota from IVM; an increase in short-chain fatty acid production was predicted by PICRUSt2 and detected with IVM treatment.}, }
@article {pmid38003306, year = {2023}, author = {Xiong, Q and Yang, J and Ni, S}, title = {Microbiome-Mediated Protection against Pathogens in Woody Plants.}, journal = {International journal of molecular sciences}, volume = {24}, number = {22}, pages = {}, doi = {10.3390/ijms242216118}, pmid = {38003306}, issn = {1422-0067}, support = {2022YFD2201900, 2021YDF22011202//National Key Research and Development Program/ ; 32122056, 42011045, 31600512//National Natural Science Foundation of China/ ; CX-21-3045//Jiangsu Agriculture Science and Technology Independent Innovation Fund/ ; 2021M691605//China Postdoctoral Science Foundation/ ; 2021K641C//Postdoctoral Science Foundation of Jiangsu Province/ ; SJCX23_0350//Postgraduate Research &amp; Practice Innovation Program of Jiangsu Province/ ; 2022NFUSPITP0364&#xff0c;202310298135Y//Students Practice Innovation and Training Program of Nanjing Forestry University/ ; }, abstract = {Pathogens, especially invasive species, have caused significant global ecological, economic, and social losses in forests. Plant disease research has traditionally focused on direct interactions between plants and pathogens in an appropriate environment. However, recent research indicates that the microbiome can interact with the plant host and pathogens to modulate plant resistance or pathogen pathogenicity, thereby altering the outcome of plant-pathogen interactions. Thus, this presents new opportunities for studying the microbial management of forest diseases. Compared to parallel studies on human and crop microbiomes, research into the forest tree microbiome and its critical role in forest disease progression has lagged. The rapid development of microbiome sequencing and analysis technologies has resulted in the rapid accumulation of a large body of evidence regarding the association between forest microbiomes and diseases. These data will aid the development of innovative, effective, and environmentally sustainable methods for the microbial management of forest diseases. Herein, we summarize the most recent findings on the dynamic structure and composition of forest tree microbiomes in belowground and aboveground plant tissues (i.e., rhizosphere, endosphere, and phyllosphere), as well as their pleiotropic impact on plant immunity and pathogen pathogenicity, highlighting representative examples of biological control agents used to modulate relevant tree microbiomes. Lastly, we discuss the potential application of forest tree microbiomes in disease control as well as their future prospects and challenges.}, }
@article {pmid38003242, year = {2023}, author = {Hardman, SJ and Shackley, FM and Ugonna, K and Darton, TC and Rigby, AS and Bogaert, D and Binkowska, JM and Condliffe, AM}, title = {Seasonal Azithromycin Use in Paediatric Protracted Bacterial Bronchitis Does Not Promote Antimicrobial Resistance but Does Modulate the Nasopharyngeal Microbiome.}, journal = {International journal of molecular sciences}, volume = {24}, number = {22}, pages = {}, doi = {10.3390/ijms242216053}, pmid = {38003242}, issn = {1422-0067}, support = {1589//Sir Halley Stewart Trust/ ; ANTSRG 03/2018//Antibiotic Research UK/ ; NIHR200636//Florey Institute AMR Research Capital Funding/ ; 50059609//Bassetlaw Fellowship Scheme/ ; }, abstract = {Protracted bacterial bronchitis (PBB) causes chronic wet cough for which seasonal azithromycin is increasingly used to reduce exacerbations. We investigated the impact of seasonal azithromycin on antimicrobial resistance and the nasopharyngeal microbiome. In an observational cohort study, 50 children with PBB were enrolled over two consecutive winters; 25/50 at study entry were designated on clinical grounds to take azithromycin over the winter months and 25/50 were not. Serial nasopharyngeal swabs were collected during the study period (12-20 months) and cultured bacterial isolates were assessed for antimicrobial susceptibility. 16S rRNA-based sequencing was performed on a subset of samples. Irrespective of azithromycin usage, high levels of azithromycin resistance were found; 73% of bacteria from swabs in the azithromycin group vs. 69% in the comparison group. Resistance was predominantly driven by azithromycin-resistant S. pneumoniae, yet these isolates were mostly erythromycin susceptible. Analysis of 16S rRNA-based sequencing revealed a reduction in within-sample diversity in response to azithromycin, but only in samples of children actively taking azithromycin at the time of swab collection. Actively taking azithromycin at the time of swab collection significantly contributed to dissimilarity in bacterial community composition. The discrepancy between laboratory detection of azithromycin and erythromycin resistance in the S. pneumoniae isolates requires further investigation. Seasonal azithromycin for PBB did not promote antimicrobial resistance over the study period, but did perturb the microbiome.}, }
@article {pmid38003202, year = {2023}, author = {Clough, J and Schwab, S and Mikac, K}, title = {Gut Microbiome Profiling of the Endangered Southern Greater Glider (Petauroides volans) after the 2019-2020 Australian Megafire.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {22}, pages = {}, doi = {10.3390/ani13223583}, pmid = {38003202}, issn = {2076-2615}, support = {Regional Bushfire Recovery for Multiregional Species and Strategic Projects Program (2021-2022)//Australian Department of Industry, Science, Energy and Resources/ ; }, abstract = {Studying the gut microbiome can provide valuable insights into animal health and inform the conservation management of threatened wildlife. Gut microbiota play important roles in regulating mammalian host physiology, including digestion, energy metabolism and immunity. Dysbiosis can impair such physiological processes and compromise host health, so it is essential that the gut microbiome be considered in conservation planning. The southern greater glider (Petauroides volans) is an endangered arboreal marsupial that faced widespread habitat fragmentation and population declines following the 2019-2020 Australian bushfire season. This study details baseline data on the gut microbiome of this species. The V3-V4 region of the 16S rRNA gene was amplified from scats collected from individuals inhabiting burnt and unburnt sites across southeastern Australia and sequenced to determine bacterial community composition. Southern greater glider gut microbiomes were characterised by high relative abundances of Firmicutes and Bacteroidota, which is consistent with that reported for other marsupial herbivores. Significant differences in gut microbial diversity and community structure were detected among individuals from different geographic locations. Certain microbiota and functional orthologues were also found to be significantly differentially abundant between locations. The role of wildfire in shaping southern greater glider gut microbiomes was shown, with some significant differences in the diversity and abundance of microbiota detected between burnt and unburnt sites. Overall, this study details the first data on greater glider (Petauroides) gut microbiomes, laying the foundation for future studies to further explore relationships between microbial community structure, environmental stressors and host health.}, }
@article {pmid38003162, year = {2023}, author = {Anderson, JG and Rojas, CA and Scarsella, E and Entrolezo, Z and Jospin, G and Hoffman, SL and Force, J and MacLellan, RH and Peak, M and Shope, BH and Tsugawa, AJ and Ganz, HH}, title = {The Oral Microbiome across Oral Sites in Cats with Chronic Gingivostomatitis, Periodontal Disease, and Tooth Resorption Compared with Healthy Cats.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {22}, pages = {}, doi = {10.3390/ani13223544}, pmid = {38003162}, issn = {2076-2615}, abstract = {Feline chronic gingivostomatitis (FCGS) is a chronic mucosal and gingival inflammatory disease in which pathogenesis remains unclear. Interactions between the host inflammatory process, the host immune response, and the oral microbiome are implicated in this pathogenesis. To begin to understand this disease and the impact of the microbiome to host inflammatory disease states, we collected sterile noninvasive plaque biofilm samples from ten distinct sites within the oral cavity in cats with stomatitis (n = 12), healthy cats (n = 9), and cats with tooth resorption or periodontitis (n = 11). Analysis of full-length 16S rRNA gene sequences indicated that the microbiomes of cats with FCGS presented marked dysbiosis at multiple oral sites. Additionally, microbiome beta diversity varied with oral condition, indicating that stomatitis, periodontitis, and/or tooth resorption influence the microbiome differently. Lastly, we found that the microbiomes of swabs taken from the oral cavity were comparable to those taken from plaque using endodontic paper points, validating this as another sampling method. Collectively, our work furthers our understanding of the dysbiosis and composition of bacteria in the oral microbiome in FCGS, with hopes of contributing to the prevention, diagnosis, and treatment of this challenging condition in felines.}, }
@article {pmid38002951, year = {2023}, author = {Diao, F and Li, Y and Gao, X and Luo, J and Zhu, X and Wang, L and Zhang, K and Li, D and Ji, J and Cui, J}, title = {Response of the Propylea japonica Microbiota to Treatment with Cry1B Protein.}, journal = {Genes}, volume = {14}, number = {11}, pages = {}, doi = {10.3390/genes14112008}, pmid = {38002951}, issn = {2073-4425}, abstract = {Propylea japonica (Thunberg) (Coleoptera: Coccinellidae) is a dominant natural enemy of insect pests in farmland ecosystems. It also serves as an important non-target insect for environmental safety evaluations of transgenic crops. Widespread planting of transgenic crops may result in direct or indirect exposure of P. japonica to recombinant Bacillus thuringiensis (Bt) protein, which may in turn affect the biological performance of this natural enemy by affecting the P. japonica microflora. However, the effects of Bt proteins (such as Cry1B) on the P. japonica microbiota are currently unclear. Here, we used a high-throughput sequencing method to investigate differences in the P. japonica microbiota resulting from treatment with Cry1B compared to a sucrose control. The results demonstrated that the P. japonica microbiome was dominated by Firmicutes at the phylum level and by Staphylococcus at the genus level. Within-sample (α) diversity indices demonstrated a high degree of consistency between the microbial communities of P. japonica treated with the sucrose control and those treated with 0.25 or 0.5 mg/mL Cry1B. Furthermore, there were no significant differences in the abundance of any taxa after treatment with 0.25 mg/mL Cry1B for 24 or 48 h, and treatment with 0.5 mg/mL Cry1B for 24 or 48 h led to changes only in Staphylococcus, a member of the phylum Firmicutes. Treatment with a high Cry1B concentration (1.0 mg/mL) for 24 or 48 h caused significant changes in the abundance of specific taxa (e.g., Gemmatimonades, Patescibacteria, Thauera, and Microbacterium). However, compared with the control, most taxa remained unchanged. The statistically significant differences may have been due to the stimulatory effects of treatment with a high concentration of Cry1B. Overall, the results showed that Cry1B protein could alter endophytic bacterial community abundance, but not composition, in P. japonica. The effects of Bt proteins on endophytes and other parameters in non-target insects require further study. This study provides data support for the safety evaluation of transgenic plants.}, }
@article {pmid38002943, year = {2023}, author = {Li, G and Yang, L and Chen, J and Zhang, X}, title = {Robust Differential Abundance Analysis of Microbiome Sequencing Data.}, journal = {Genes}, volume = {14}, number = {11}, pages = {}, doi = {10.3390/genes14112000}, pmid = {38002943}, issn = {2073-4425}, support = {R01GM144351/NH/NIH HHS/United States ; }, abstract = {It is well known that the microbiome data are ridden with outliers and have heavy distribution tails, but the impact of outliers and heavy-tailedness has yet to be examined systematically. This paper investigates the impact of outliers and heavy-tailedness on differential abundance analysis (DAA) using the linear models for the differential abundance analysis (LinDA) method and proposes effective strategies to mitigate their influence. The presence of outliers and heavy-tailedness can significantly decrease the power of LinDA. We investigate various techniques to address outliers and heavy-tailedness, including generalizing LinDA into a more flexible framework that allows for the use of robust regression and winsorizing the data before applying LinDA. Our extensive numerical experiments and real-data analyses demonstrate that robust Huber regression has overall the best performance in addressing outliers and heavy-tailedness.}, }
@article {pmid38002858, year = {2023}, author = {Bettag, J and Goldenberg, D and Carter, J and Morfin, S and Borsotti, A and Fox, J and ReVeal, M and Natrop, D and Gosser, D and Kolli, S and Jain, AK}, title = {Gut Microbiota to Microglia: Microbiome Influences Neurodevelopment in the CNS.}, journal = {Children (Basel, Switzerland)}, volume = {10}, number = {11}, pages = {}, doi = {10.3390/children10111767}, pmid = {38002858}, issn = {2227-9067}, abstract = {The brain is traditionally viewed as an immunologically privileged site; however, there are known to be multiple resident immune cells that influence the CNS environment and are reactive to extra-CNS signaling. Microglia are an important component of this system, which influences early neurodevelopment in addition to modulating inflammation and regenerative responses to injury and infection. Microglia are influenced by gut microbiome-derived metabolites, both as part of their normal function and potentially in pathological patterns that may induce neurodevelopmental disabilities or behavioral changes. This review aims to summarize the mounting evidence indicating that, not only is the Gut-Brain axis mediated by metabolites and microglia throughout an organism's lifetime, but it is also influenced prenatally by maternal microbiome and diet, which holds implications for both early neuropathology and neurodevelopment.}, }
@article {pmid38002796, year = {2023}, author = {Wong, PY and Yip, C and Lemberg, DA and Day, AS and Leach, ST}, title = {Evolution of a Pathogenic Microbiome.}, journal = {Journal of clinical medicine}, volume = {12}, number = {22}, pages = {}, doi = {10.3390/jcm12227184}, pmid = {38002796}, issn = {2077-0383}, abstract = {The process of microbiome development arguably begins before birth. Vertical transmission of bacteria from the mother to the infant is a keystone event in microbiome development. Subsequent to birth, the developing microbiome is vulnerable to influence from a wide range of factors. Additionally, the microbiome can influence the health and development of the host infant. This intricate interaction of the gastrointestinal microbiome and the host has been described as both symbiotic and dysbiotic. Defining these terms, a symbiotic microbiome is where the microbiome and host provide mutual benefit to each other. A pathogenic microbiome, or more precisely a gastrointestinal microbiome associated with disease, is increasing described as dysbiotic. This review seeks to investigate the factors that contribute to evolving a disease-causing or 'dysbiotic' microbiome. This review covers the development of the gastrointestinal microbiome in infants, the interaction of the microbiome with the host, and its contribution to host immunity and investigates specific features of the gastrointestinal microbiome that are associated with disease.}, }
@article {pmid38002788, year = {2023}, author = {Velho, RV and Werner, F and Mechsner, S}, title = {Endo Belly: What Is It and Why Does It Happen?-A Narrative Review.}, journal = {Journal of clinical medicine}, volume = {12}, number = {22}, pages = {}, doi = {10.3390/jcm12227176}, pmid = {38002788}, issn = {2077-0383}, abstract = {Endometriosis is a chronic inflammatory disease where endometrial-like lesions settle outside the uterus, resulting in extensive inflammatory reactions. It is a complex disease that presents with a range of symptoms, with pain and infertility being the most common. Along with severe dysmenorrhea, cyclic and acyclic lower abdominal pain, cyclic dysuria and dyschezia, dyspareunia, and infertility, there are also nonspecific complaints that can cause confusion and make endometriosis the chameleon among gynecological diseases. These symptoms include unspecific intestinal complaints, cyclic diarrhea, but also constipation, nausea, vomiting, and stomach complaints. It appears that in addition to general bowel symptoms, there are also specific symptoms related to endometriosis such as cyclic bloating of the abdomen, known as endo belly. During the second half of the menstrual cycle leading up to menstruation, the abdomen becomes increasingly bloated causing discomfort and pain due to elevated sensitivity of the intestinal wall. Patients with endometriosis exhibit a reduced stretch pain threshold of the intestinal wall. Here, we review the endo belly, for the first time, pathophysiology and the influence of other diseases (such as irritable bowel syndrome-IBS), microbiome, hormonal levels, inflammation, and diet on the presentation of this condition.}, }
@article {pmid38002515, year = {2023}, author = {Kulkarni, MS and Miller, BC and Mahani, M and Mhaskar, R and Tsalatsanis, A and Jain, S and Yadav, H}, title = {Poor Oral Health Linked with Higher Risk of Alzheimer's Disease.}, journal = {Brain sciences}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/brainsci13111555}, pmid = {38002515}, issn = {2076-3425}, abstract = {Alzheimer's disease (AD) is a multifactorial neurodegenerative disease characterized by cognitive and behavioral changes in older adults. Emerging evidence suggests poor oral health is associated with AD, but there is a lack of large-scale clinical studies demonstrating this link. Herein, we used the TriNetX database to generate clinical cohorts and assess the risk of AD and survival among >30 million de-identified subjects with normal oral health (n = 31,418,814) and poor oral health (n = 1,232,751). There was a greater than two-fold increase in AD risk in the poor oral health cohort compared to the normal oral health group (risk ratio (RR): 2.363, (95% confidence interval: 2.326, 2.401)). To reduce potential bias, we performed retrospective propensity score matching for age, gender, and multiple laboratory measures. After matching, the cohorts had no significant differences in survival probability. Furthermore, when comparing multiple oral conditions, diseases related to tooth loss were the most significant risk factor for AD (RR: 3.186, (95% CI: 3.007, 3.376)). Our results suggest that oral health may be important in AD risk, regardless of age, gender, or laboratory measures. However, more large-scale cohort studies are necessary to validate these findings and further evaluate links between oral health and AD.}, }
@article {pmid38002290, year = {2023}, author = {Saha, S and Boesch, C and Maycock, J and Wood, S and Do, T}, title = {Sweet Orange Juice Processing By-Product Extracts: A Caries Management Alternative to Chlorhexidine.}, journal = {Biomolecules}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/biom13111607}, pmid = {38002290}, issn = {2218-273X}, abstract = {Dental caries is one of the most prevalent chronic diseases globally in both children and adults. This study investigated the potential of industrial sweet orange waste extracts (ISOWE) as a substitute for chlorhexidine (CHX) in managing dental caries. First, the cytotoxicity of ISOWE (40, 80, 120 mg/mL) and CHX (0.1 and 0.2%) on buccal epithelial cells was determined. ISOWE exhibited no overall toxicity, whereas CHX strongly affected cell viability. The combination of ISOWE and CHX significantly enhanced cell proliferation compared to CHX alone. Next, the antimicrobial efficacy of ISOWE, CHX, and their combination was assessed against a 7-day complex biofilm model inoculated with oral samples from human volunteers. CHX exhibited indiscriminate antimicrobial action, affecting both pathogenic and health-associated oral microorganisms. ISOWE demonstrated lower antimicrobial efficacy than CHX but showed enhanced efficacy against pathogenic species while preserving the oral microbiome's balance. When applied to a cariogenic biofilm, the combined treatment of ISOWE with 0.1% CHX showed similar efficacy to 0.2% CHX treatment alone. Overall, the findings suggest that ISOWE is a promising natural anti-cariogenic agent with lower toxicity and enhanced selectivity for pathogenic species compared to CHX.}, }
@article {pmid38002184, year = {2023}, author = {Tang, Z and Zhan, L and He, R and Zhou, Y and Tang, Q and Liu, Z and Zhang, S and Liu, A}, title = {Hepatoprotective Effect of Tea Composite Solid Beverage on Alcohol-Caused Rat Liver Injury.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {22}, pages = {}, doi = {10.3390/foods12224126}, pmid = {38002184}, issn = {2304-8158}, support = {2022YFE011120 &amp; 2021YFD1601104//National Key R&amp;D Project/ ; 2021NK1020-3//Key R&amp;D Project of Hunan Province/ ; No. 2021JJ40251//Natural Science Foundation of Hunan Province Youth Fund/ ; }, abstract = {Alcoholic liver disease (ALD) remains a major cause of liver-related morbidity and mortality worldwide. Tea polyphenols (TPs) possess strong antioxidant activity; cassia seed extract (CSE) has the effect of brightening the eyes; and Ampelopsis grossedentata extract (AGE) has the function of protecting the liver. However, the synergistic hepatoprotective effect of TP, AGE and CSE as a joint formulation is unknown. This study aimed to investigate the role of a tea solid beverage, composed of TP, AGE and CSE, on chronic alcoholic liver injury in rats and its underlying mechanisms via the analysis of transcriptomics and gut microbiota. The histopathological findings revealed that the tea solid beverage could reduce the production of fat vacuoles and inflammatory cell infiltration. Additionally, the tea solid beverage was found to effectively relieve the increase in the AST (from 424.85 U/L to 180.17 U/L), ALT (from 139.95 U/L to 85.88 U/L) and LDH (from 21.16 U/L to 13.35 U/L) enzyme activities and the expression of the inflammatory factors TNF-α (from 394.02 pg/mL to 214.44 pg/mL) and IL-6 (from 208.46 pg/mL to 116.59 pg/mL) caused by alcohol consumption. Further, it significantly enhanced the GSH concentration (from 4.53 pg/mL to 8.08 pg/mL) and SOD activity (from 84.70 U/mL to 156.94 U/mL) and decreased the MDA (from 58.61 mmol/mL to 36.58 mmol/mL) and TG (from 7.07 mmol/L to 3.43 mmol/L)) concentrations in the liver of rats. The analysis and identification of transcriptomics showed that the tea solid beverage intervention primarily protected the liver of rats with chronic alcoholic injury by up-regulating the differential gene Hmgcs1 in order to increase the synthesis of ketone bodies and by down-regulating the differential gene Pfkfb1 for the purpose of decreasing the glucose metabolism. Additionally, it was found that the tea solid beverage could significantly change the composition of intestinal flora in drinking rats by regulating mineral absorption, the pathways of bile secretion, the adipocytokine signaling pathway and the peroxisome balance of the intestinal flora, in order to protect alcohol-drinking rats' livers. In conclusion, the tea solid beverage, consisting of TP, AGE and CSE, is a functional drink that prevents ketone metabolism, glucose metabolism and microbiome disorders induced by alcohol intake.}, }
@article {pmid38002033, year = {2023}, author = {Altamura, S and Pietropaoli, D and Lombardi, F and Del Pinto, R and Ferri, C}, title = {An Overview of Chronic Kidney Disease Pathophysiology: The Impact of Gut Dysbiosis and Oral Disease.}, journal = {Biomedicines}, volume = {11}, number = {11}, pages = {}, doi = {10.3390/biomedicines11113033}, pmid = {38002033}, issn = {2227-9059}, support = {DK042191-S1/NH/NIH HHS/United States ; }, abstract = {Chronic kidney disease (CKD) is a severe condition and a significant public health issue worldwide, carrying the burden of an increased risk of cardiovascular events and mortality. The traditional factors that promote the onset and progression of CKD are cardiometabolic risk factors like hypertension and diabetes, but non-traditional contributors are escalating. Moreover, gut dysbiosis, inflammation, and an impaired immune response are emerging as crucial mechanisms in the disease pathology. The gut microbiome and kidney disease exert a reciprocal influence commonly referred to as "the gut-kidney axis" through the induction of metabolic, immunological, and endocrine alterations. Periodontal diseases are strictly involved in the gut-kidney axis for their impact on the gut microbiota composition and for the metabolic and immunological alterations occurring in and reciprocally affecting both conditions. This review aims to provide an overview of the dynamic biological interconnections between oral health status, gut, and renal pathophysiology, spotlighting the dynamic oral-gut-kidney axis and raising whether periodontal diseases and gut microbiota can be disease modifiers in CKD. By doing so, we try to offer new insights into therapeutic strategies that may enhance the clinical trajectory of CKD patients, ultimately advancing our quest for improved patient outcomes and well-being.}, }
@article {pmid38001930, year = {2023}, author = {Boicean, A and Birlutiu, V and Ichim, C and Brusnic, O and Onișor, DM}, title = {Fecal Microbiota Transplantation in Liver Cirrhosis.}, journal = {Biomedicines}, volume = {11}, number = {11}, pages = {}, doi = {10.3390/biomedicines11112930}, pmid = {38001930}, issn = {2227-9059}, abstract = {The human gastrointestinal tract houses a diverse array of probiotic and pathogenic bacteria and any alterations in this microbial composition can exert a significant influence on an individual's well-being. It is well-established that imbalances in the gut microbiota play a pivotal role in the development of liver diseases. In light of this, a new adjuvant therapy for liver diseases could be regulating the intestinal microbiota. Through fecal microbiota transplantation, patients whose microbiomes are compromised are treated with stool from healthy donors in an attempt to restore a normal microbiome and alleviate their symptoms. A review of cross-sectional studies and case reports suggests that fecal microbiota transplants may offer effective treatment for chronic liver diseases. Adding to the potential of this emerging therapy, recent research has indicated that fecal microbiota transplantation holds promise as a therapeutic approach specifically for liver cirrhosis. By introducing a diverse range of beneficial microorganisms into the gut, this innovative treatment aims to address the microbial imbalances often observed in cirrhotic patients. While further validation is still required, these preliminary findings highlight the potential impact of fecal microbiota transplantation as a novel and targeted method for managing liver cirrhosis. We aimed to summarize the current state of understanding regarding this procedure, as a new therapeutic method for liver cirrhosis, as well as to explain its clinical application and future potential.}, }
@article {pmid38001694, year = {2023}, author = {Maghsoudi, H and Sheikhnia, F and Sitarek, P and Hajmalek, N and Hassani, S and Rashidi, V and Khodagholi, S and Mir, SM and Malekinejad, F and Kheradmand, F and Ghorbanpour, M and Ghasemzadeh, N and Kowalczyk, T}, title = {The Potential Preventive and Therapeutic Roles of NSAIDs in Prostate Cancer.}, journal = {Cancers}, volume = {15}, number = {22}, pages = {}, doi = {10.3390/cancers15225435}, pmid = {38001694}, issn = {2072-6694}, abstract = {Prostate cancer (PC) is the second most common type of cancer and the leading cause of death among men worldwide. Preventing the progression of cancer after treatments such as radical prostatectomy, radiation therapy, and hormone therapy is a major concern faced by prostate cancer patients. Inflammation, which can be caused by various factors such as infections, the microbiome, obesity and a high-fat diet, is considered to be the main cause of PC. Inflammatory cells are believed to play a crucial role in tumor progression. Therefore, nonsteroidal anti-inflammatory drugs along with their effects on the treatment of inflammation-related diseases, can prevent cancer and its progression by suppressing various inflammatory pathways. Recent evidence shows that nonsteroidal anti-inflammatory drugs are effective in the prevention and treatment of prostate cancer. In this review, we discuss the different pathways through which these drugs exert their potential preventive and therapeutic effects on prostate cancer.}, }
@article {pmid38001645, year = {2023}, author = {Tu, SM and Aydin, AM and Maraboyina, S and Chen, Z and Singh, S and Gokden, N and Langford, T}, title = {Stem Cell Origin of Cancer: Clinical Implications for Cancer Immunity and Immunotherapy.}, journal = {Cancers}, volume = {15}, number = {22}, pages = {}, doi = {10.3390/cancers15225385}, pmid = {38001645}, issn = {2072-6694}, abstract = {A simple way to understand the immune system is to separate the self from non-self. If it is self, the immune system tolerates and spares. If it is non-self, the immune system attacks and destroys. Consequently, if cancer has a stem cell origin and is a stem cell disease, we have a serious problem and a major dilemma with immunotherapy. Because many refractory cancers are more self than non-self, immunotherapy may become an uphill battle and pyrrhic victory in cancer care. In this article, we elucidate cancer immunity. We demonstrate for whom, with what, as well as when and how to apply immunotherapy in cancer care. We illustrate that a stem cell theory of cancer affects our perspectives and narratives of cancer. Without a pertinent theory about cancer's origin and nature, we may unwittingly perform misdirected cancer research and prescribe misguided cancer treatments. In the ongoing saga of immunotherapy, we are at a critical juncture. Because of the allure and promises of immunotherapy, we will be treating more patients not immediately threatened by their cancer. They may have more to lose than to gain, if we have a misconception and if we are on a wrong mission with immunotherapy. According to the stem cell theory of cancer, we should be careful with immunotherapy. When we do not know or realize that cancer originates from a stem cell and has stem-ness capabilities, we may cause more harm than good in some patients and fail to separate the truth from the myth about immunotherapy in cancer care.}, }
@article {pmid38001408, year = {2023}, author = {Chen, C and Zhang, Y and Yao, X and Yan, Q and Li, S and Zhong, Q and Liu, Z and Tang, F and Liu, C and Li, H and Zhu, D and Lan, W and Ling, Y and Lu, D and Xu, H and Ning, Q and Wang, Y and Jiang, Z and Zhang, Q and Gu, G and Sun, L and Wang, N and Wang, G and Zhang, A and Ullah, H and Sun, W and Ma, W}, title = {Characterizations of the multi-kingdom gut microbiota in Chinese patients with gouty arthritis.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {363}, pmid = {38001408}, issn = {1471-2180}, support = {Support [2020]4Y155//Science and Technology Program of Guizhou Province/ ; Platform and talent [2020]2202//Science and Technology Program of Guizhou Province/ ; 82260894//National Natural Science Foundation of China/ ; 81902037//National Natural Science Foundation of China/ ; GZEYK-B[2021]2//Scientific Research Project of the Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine/ ; }, abstract = {OBJECTIVE: The gut microbial composition has been linked to metabolic and autoimmune diseases, including arthritis. However, there is a dearth of knowledge on the gut bacteriome, mycobiome, and virome in patients with gouty arthritis (GA).<br><br>METHODS: We conducted a comprehensive analysis of the multi-kingdom gut microbiome of 26 GA patients and 28 healthy controls, using whole-metagenome shotgun sequencing of their stool samples.<br><br>RESULTS: Profound alterations were observed in the gut bacteriome, mycobiome, and virome of GA patients. We identified 1,117 differentially abundant bacterial species, 23 fungal species, and 4,115 viral operational taxonomic units (vOTUs). GA-enriched bacteria included Escherichia coli_D GENOME144544, Bifidobacterium infantis GENOME095938, Blautia_A wexlerae GENOME096067, and Klebsiella pneumoniae GENOME147598, while control-enriched bacteria comprised Faecalibacterium prausnitzii_G GENOME147678, Agathobacter rectalis GENOME143712, and Bacteroides_A plebeius_A GENOME239725. GA-enriched fungi included opportunistic pathogens like Cryptococcus neoformans GCA_011057565, Candida parapsilosis GCA_000182765, and Malassezia spp., while control-enriched fungi featured several Hortaea werneckii subclades and Aspergillus fumigatus GCA_000002655. GA-enriched vOTUs mainly attributed to Siphoviridae, Myoviridae, Podoviridae, and Microviridae, whereas control-enriched vOTUs spanned 13 families, including Siphoviridae, Myoviridae, Podoviridae, Quimbyviridae, Phycodnaviridae, and crAss-like. A co-abundance network revealed intricate interactions among these multi-kingdom signatures, signifying their collective influence on the disease. Furthermore, these microbial signatures demonstrated the potential to effectively discriminate between patients and controls, highlighting their diagnostic utility.<br><br>CONCLUSIONS: This study yields crucial insights into the characteristics of the GA microbiota that may inform future mechanistic and therapeutic investigations.}, }
@article {pmid38000818, year = {2023}, author = {Weber, AM and Barbazza, S and Fauzi, MD and Rachmadewi, A and Zuhrina, R and Putri, FK and Campos Ponce, M and Hoeven, MV and Rimbawan, R and Nasution, Z and Giriwono, PE and Wieringa, FT and Soekarjo, DD and Ryan, EP}, title = {Solutions to Enhance Health with Alternative Treatments (SEHAT) protocol: a double-blinded randomised controlled trial for gut microbiota-targeted treatment of severe acute malnutrition using rice bran in ready-to-use therapeutic foods in Indonesia.}, journal = {BMJ open}, volume = {13}, number = {11}, pages = {e076805}, doi = {10.1136/bmjopen-2023-076805}, pmid = {38000818}, issn = {2044-6055}, abstract = {INTRODUCTION: Current formulations of ready-to-use therapeutic foods (RUTFs) to treat severe acute malnutrition (SAM) in children focus on nutrient density and quantity. Less attention is given to foods targeting gut microbiota metabolism and mucosal barrier functions. Heat-stabilised rice bran contains essential nutrients, prebiotics, vitamins and unique phytochemicals that have demonstrated favourable bioactivity to modulate gut microbiota composition and mucosal immunity. This study seeks to examine the impact of RUTF with rice bran on the microbiota during SAM treatment, recovery and post-treatment growth outcomes in Jember, Indonesia. Findings are expected to provide insights into rice bran as a novel food ingredient to improve SAM treatment outcomes.<br><br>METHODS AND ANALYSIS: A total of 200 children aged 6-59 months with uncomplicated SAM (weight-for-height z-scores (WHZ) <-3, or mid-upper arm circumference (MUAC) <115&#x2009;mm or having bilateral pitting oedema +/++) or approaching SAM (WHZ<-2.5) will be enrolled in a double-blinded, randomised controlled trial. Children in the active control arm will receive a locally produced RUTF; those in the intervention arm will receive the local RUTF with 5% rice bran. Children will receive daily RUTF treatment for 8 weeks and be monitored for 8 weeks of follow-up. Primary outcomes include the effectiveness of RUTF as measured by changes in weight, WHO growth z-scores, MUAC and morbidity. Secondary outcomes include modulation of the gut microbiome and dried blood spot metabolome, the percentage of children recovered at weeks 8 and 12, and malnutrition relapse at week 16. An intention-to-treat analysis will be conducted for each outcome.<br><br>ETHICS AND DISSEMINATION: The findings of this trial will be submitted to peer-reviewed journals and will be presented at relevant conferences. Ethics approval obtained from the Medical and Health Research Ethical Committee at the Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Madain Yogyakarta Ref. No.: KE/FK/0546/EC/2022 and KE/FK/0703/EC/2023 and from Colorado State University IRB#1823, OHRP FWA00000647.<br><br>TRIAL REGISTRATION NUMBER: NCT05319717.}, }
@article {pmid38000743, year = {2023}, author = {Reiß, F and Kiefer, N and Purahong, W and Borken, W and Kalkhof, S and Noll, M}, title = {Active soil microbial composition and proliferation are directly affected by the presence of biocides from building materials.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {168689}, doi = {10.1016/j.scitotenv.2023.168689}, pmid = {38000743}, issn = {1879-1026}, abstract = {Combinations of biocides are commonly added to building materials to prevent microbial growth and thereby cause degradation of the façades. These biocides reach the environment by leaching from façades posing an environmental risk. Although ecotoxicity to the aquatic habitat is well established, there is hardly any data on the ecotoxicological effects of biocides on the soil habitat. This study aimed to characterize the effect of the biocides terbutryn, isoproturon, octhilinone, and combinations thereof on the total and active soil microbial community composition and functions. Total soil microbial community was retrieved directly from the nucleic acid extracts, while the DNA of the active soil microbial community was separated after bromodeoxyuridine labeling. Bacterial 16S rRNA gene and fungal transcribed spacer region gene-based amplicon sequencing was carried out for both active and total, while gene copy numbers were quantified only for the total soil microbial community. Additionally, soil respiration and physico-chemical parameters were analyzed to investigate overall soil microbial activity. The bacterial and fungal gene copy numbers were significantly affected by single biocides and combined biocide soil treatment but not soil respiration and physico-chemical parameters. Moreover, results showed that single and combined biocide treatment only had minor effects on the total soil microbiome. While the total soil microbiome experienced only minor effects from single and combined biocide treatment, the active soil microbiome was significantly impacted in its diversity, richness, composition, and functional patterns. The active bacterial richness was more sensitive than fungi. However, the adverse effects of the biocide combination treatments on soil bacterial richness were highly dependent on the identities of the biocide combination. Our results demonstrate that the presence of biocides frequently used in building materials affects the active soil microbiome. Thereby, the approach described herein can be used as an ecotoxicological measure for the effect on complex soil environments in future studies.}, }
@article {pmid38001502, year = {2023}, author = {Li, P and Hong, J and Yuan, Z and Huang, Y and Wu, M and Ding, T and Wu, Z and Sun, X and Lin, D}, title = {Gut microbiota in parasite-transmitting gastropods.}, journal = {Infectious diseases of poverty}, volume = {12}, number = {1}, pages = {105}, pmid = {38001502}, issn = {2049-9957}, support = {2020YFC1200100//the National Key R&amp;D Program of China/ ; 2020YFC1200103//the National Key R&amp;D Program of China/ ; 2021YFC2300800//the National Key R&amp;D Program of China/ ; 2016YFC1200500//the National Key R&amp;D Program of China/ ; 82202560//the National Natural Science Foundation of China/ ; 82161160343//the National Natural Science Foundation of China/ ; 82272361//the National Natural Science Foundation of China/ ; 2021B1212040017//the Science and Technology Planning Project of Guangdong Province/ ; 2022B1111030002//the R&amp;D Program in Key Areas of Guangdong Province/ ; 22qntd4813//the Fundamental Research Funds for the Central University/ ; B12003//the 111 Project/ ; 20201192//the 6th Nuclear Energy R&amp;D Project/ ; NPRC-2019-194-30//the National Parasitic Resource Center and Ministry of Science and Technology/ ; }, abstract = {BACKGROUND: Gastropoda, the largest class within the phylum Mollusca, houses diverse gut microbiota, and some gastropods serve as intermediate hosts for parasites. Studies have revealed that gut bacteria in gastropods are associated with various biological aspects, such as growth, immunity and host-parasite interactions. Here, we summarize our current knowledge of gastropod gut microbiomes and highlight future research priorities and perspectives.<br><br>METHODS: A literature search was undertaken using PubMed, Web of Science and CNKI for the articles on the gut microbiota of gastropods until December 31, 2022. We retrieved a total of 166 articles and identified 73 eligible articles for inclusion in this review based on the inclusion and exclusion criteria.<br><br>RESULTS: Our analysis encompassed freshwater, seawater and land snails, with a specific focus on parasite-transmitting gastropods. We found that most studies on gastropod gut microbiota have primarily utilized 16S rRNA gene sequencing to analyze microbial composition, rather than employing metagenomic, metatranscriptomic, or metabolomic approaches. This comprehensive review provided an overview of the parasites carried by snail species in the context of gut microbiota studies. We presented the gut microbial trends, a comprehensive summary of the diversity and composition, influencing factors, and potential functions of gastropod gut microbiota. Additionally, we discussed the potential applications, research gaps and future perspectives of gut microbiomes in parasite-transmitting gastropods. Furthermore, several strategies for enhancing our comprehension of gut microbiomes in snails were also discussed.<br><br>CONCLUSIONS: This review comprehensively summarizes the current knowledge on the composition, potential function, influencing factors, potential applications, limitations, and challenges of gut microbiomes in gastropods, with a specific emphasis on parasite-transmitting gastropods. These findings provide important insights for future studies aiming to understand the potential role of gastropod gut microbiota in controlling snail populations and snail-borne diseases.}, }
@article {pmid38001152, year = {2023}, author = {Naddaf, R and Carasso, S and Reznick-Levi, G and Hasnis, E and Qarawani, A and Maza, I and Gefen, T and Half, EE and Geva-Zatorsky, N}, title = {Gut microbial signatures are associated with Lynch syndrome (LS) and cancer history in Druze communities in Israel.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {20677}, pmid = {38001152}, issn = {2045-2322}, abstract = {Lynch syndrome (LS) is a hereditary cancer syndrome caused by autosomal dominant mutations, with high probability of early onset for several cancers, mainly colorectal cancer (CRC). The gut microbiome was shown to be influenced by host genetics and to be altered during cancer development. Therefore, we aimed to determine alterations in gut microbiome compositions of LS patients with and without cancer. We performed fecal microbiome analyses on samples of LS and non-LS members from the Druze ethnoreligious community in Israel, based on both their LS mutation and their cancer history. Our analysis revealed specific bacterial operational taxonomic units (OTUs) overrepresented in LS individuals as well as bacterial OTUs differentiating between the LS individuals with a history of cancer. The identified OTUs align with previous studies either correlating them to pro-inflammatory functions, which can predispose to cancer, or to the cancer itself, and as such, these bacteria can be considered as future therapeutic targets.}, }
@article {pmid38001080, year = {2023}, author = {Choi, W and Mangal, U and Park, JY and Kim, JY and Jun, T and Jung, JW and Choi, M and Jung, S and Lee, M and Na, JY and Ryu, DY and Kim, JM and Kwon, JS and Koh, WG and Lee, S and Hwang, PTJ and Lee, KJ and Jung, UW and Cha, JK and Choi, SH and Hong, J}, title = {Occlusive membranes for guided regeneration of inflamed tissue defects.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7687}, pmid = {38001080}, issn = {2041-1723}, support = {KRIT-CT-21-034//Ministry of National Defense, Republic of Korea | Defense Acquisition Program Administration (DAPA)/ ; NRF-2022K2A9A1A0609182711//National Research Foundation of Korea (NRF)/ ; HI22C1609//Ministry of Health and Welfare (Ministry of Health, Welfare and Family Affairs)/ ; }, abstract = {Guided bone regeneration aided by the application of occlusive membranes is a promising therapy for diverse inflammatory periodontal diseases. Symbiosis, homeostasis between the host microbiome and cells, occurs in the oral environment under normal, but not pathologic, conditions. Here, we develop a symbiotically integrating occlusive membrane by mimicking the tooth enamel growth or multiple nucleation biomineralization processes. We perform human saliva and in vivo canine experiments to confirm that the symbiotically integrating occlusive membrane induces a symbiotic healing environment. Moreover, we show that the membrane exhibits tractability and enzymatic stability, maintaining the healing space during the entire guided bone regeneration therapy period. We apply the symbiotically integrating occlusive membrane to treat inflammatory-challenged cases in vivo, namely, the open and closed healing of canine premolars with severe periodontitis. We find that the membrane promotes symbiosis, prevents negative inflammatory responses, and improves cellular integration. Finally, we show that guided bone regeneration therapy with the symbiotically integrating occlusive membrane achieves fast healing of gingival soft tissue and alveolar bone.}, }
@article {pmid38000973, year = {2023}, author = {Armstrong, PA and Venugopal, N and Wright, TJ and Randolph, KM and Batson, RD and Yuen, KCJ and Masel, BE and Sheffield-Moore, M and Urban, RJ and Pyles, RB}, title = {Traumatic brain injury, abnormal growth hormone secretion, and gut dysbiosis.}, journal = {Best practice &amp; research. Clinical endocrinology &amp; metabolism}, volume = {}, number = {}, pages = {101841}, doi = {10.1016/j.beem.2023.101841}, pmid = {38000973}, issn = {1878-1594}, abstract = {The gut microbiome has been implicated in a variety of neuropathologies with recent data suggesting direct effects of the microbiome on host metabolism, hormonal regulation, and pathophysiology. Studies have shown that gut bacteria impact host growth, partially mediated through the growth hormone (GH)/insulin-like growth factor 1 (IGF-1) axis. However, no study to date has examined the specific role of GH on the fecal microbiome (FMB) or the changes in this relationship following a traumatic brain injury (TBI). Current literature has demonstrated that TBI can lead to either temporary or sustained abnormal GH secretion (aGHS). More recent literature has suggested that gut dysbiosis may contribute to aGHS leading to long-term sequelae now known as brain injury associated fatigue and cognition (BIAFAC). The aGHS observed in some TBI patients presents with a symptom complex including profound fatigue and cognitive dysfunction that improves significantly with exogenous recombinant human GH treatment. Notably, GH treatment is not curative as fatigue and cognitive decline typically recur upon treatment cessation, indicating the need for additional studies to address the underlying mechanistic cause.}, }
@article {pmid38000798, year = {2023}, author = {Wadhwani, R and Williams, A}, title = {Protect the Microbiome: Be HOLISTIC.}, journal = {Neonatal network : NN}, volume = {42}, number = {6}, pages = {342-347}, doi = {10.1891/NN-2023-0001}, pmid = {38000798}, issn = {1539-2880}, abstract = {The newborn who requires intensive care hospitalization is forced into an external environment that can negatively impact the developing microbiome. The NICU nurse has a unique role that affects, and may even protect, the development of the newborn microbiome through daily nursing care. The purpose of this article is to inform neonatal nurses regarding common nursing interventions that can positively or negatively impact the developing microbiome. Evidence-based practices are presented and bundled to describe their impact the neonatal microbiome.}, }
@article {pmid38000749, year = {2023}, author = {Lewin, S and Wende, S and Wehrhan, M and Verch, G and Ganugi, P and Sommer, M and Kolb, S}, title = {Cereals rhizosphere microbiome undergoes host selection of nitrogen cycle guilds correlated to crop productivity.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {168794}, doi = {10.1016/j.scitotenv.2023.168794}, pmid = {38000749}, issn = {1879-1026}, abstract = {Sustainable transformation of agricultural plant production requires the reduction of nitrogen (N) fertilizer application. Such a reduced N fertilizer application may impede crop production due to an altered symbiosis of crops and their rhizosphere microbiome, since reduced N input may affect the competition and synergisms with the plant. The assessment of such changes in the crop microbiome functionalities at spatial scales relevant for agricultural management remains challenging. We investigated in a field plot experiment how and if the N cycling guilds of the rhizosphere of globally relevant cereal crops - winter barley, wheat and rye - are influenced by reduced N fertilization. Crop productivity was assessed by remote sensing of the shoot biomass. Microbial N cycling guilds were investigated by metagenomics targeting diazotrophs, nitrifiers, denitrifiers and the dissimilatory nitrate to ammonium reducing guild (DNRA). The functional composition of microbial N cycling guilds was explained by crop productivity parameters and soil pH, and diverged substantially between the crop species. The responses of individual microbial N cycling guild abundances to shoot dry weight and rhizosphere nitrate content was modulated by the N fertilization treatments and the crop species, which was identified based on regression analyses. Thus, characteristic shifts in the microbial N cycling guild acquisition associated with the crop host species were resolved. Particularly, the rhizosphere of rye was enriched with potentially N-preserving microbial guilds - diazotrophs and the DNRA guild - when no fertilizer was applied. We speculate that the acquisition of microbial N cycling guilds was the result of plant species-specific acquisition strategies. Thus, the investigated cereal crop holobionts have likely different symbiotic strategies that make them differently resilient against reduced N fertilizer inputs. Furthermore, we demonstrated that these belowground patterns of N cycling guilds from the rhizosphere microbiome are linked to remotely sensed aboveground plant productivity.}, }
@article {pmid38000633, year = {2023}, author = {Hou, J and Lam, KL and Chiu, YT and Kwong, KY and Lau, HL and Marafa, LM and Tsui, SKW and Mo, IWY and Chan, PL}, title = {Urban green waste bulking agent is the major source of antimicrobial resistance genes persisted in home compost, not animal manure.}, journal = {Environmental research}, volume = {}, number = {}, pages = {117713}, doi = {10.1016/j.envres.2023.117713}, pmid = {38000633}, issn = {1096-0953}, abstract = {Urban green waste and food waste are often used as bulking agents to prepare home compost in combination with animal manure in urban horticulture and community gardening. Although it is known that antimicrobial resistance genes (ARGs) persist in home compost, their origins have not been determined. In addition, the factors contributing to ARGs persistence remain unclear. In this study, we aim to (i) characterize the changes in the microbiome and antimicrobial resistome during the composting process of home compost using metagenomics shotgun sequencing, (ii) identify the source of the ARGs persisted in home compost using SourceTracker, and (iii) elucidate the collective effect of compost microbiome and environmental factors, including the physicochemical properties and antibiotics concentration of home compost, in contributing to ARG persistence using Procrustes analysis, co-occurrence network analysis, variation partitioning analysis, and structural equation modeling. SourceTracker analysis indicated that urban green waste bulking agent was the major source of the persisting ARGs in home compost instead of animal manure. Procrustes analysis and co-occurrence network analysis revealed a strong association between microbiome and antimicrobial resistome. Variation partitioning analysis and structural equation modeling suggested that physicochemical properties shaped the antimicrobial resistome directly and indirectly by influencing the microbiome. Our results indicated that the persistence of ARGs in home compost might be due to the succession of microbial species from the urban green waste bulking agent, and the physicochemical properties might have defined the compost environment to shape the microbiome in the compost, thus, in turn, the persisting antimicrobial resistome. (248 words).}, }
@article {pmid38000281, year = {2023}, author = {Bombaywala, S and Bajaj, A and Dafale, NA}, title = {Deterministic effect of oxygen level variation on shaping antibiotic resistome.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133047}, doi = {10.1016/j.jhazmat.2023.133047}, pmid = {38000281}, issn = {1873-3336}, abstract = {An increase in acquisition of antibiotic resistance genes (ARGs) by pathogens under antibiotic selective pressure poses public health threats. Sub-inhibitory antibiotics induce bacteria to generate reactive oxygen species (ROS) dependent on dissolved oxygen (DO) levels, while molecular connection between ROS-mediated ARG emergence through DNA damage and metabolic changes remains elusive. Thus, the study investigates antibiotic resistome dynamics, microbiome shift, and pathogen distribution in hyperoxic (5-7 mg L[-1]), normoxic (2-4 mg L[-1]), and hypoxic (0.5-1 mg L[-1]) conditions using lab-scale bioreactor. Composite inoculums in the reactor were designed to represent comprehensive microbial community and AR profile from selected activated sludge. RT-qPCR and metagenomic analysis showed an increase in ARG count (100.98 ppm) with enrichment of multidrug efflux pumps (acrAB, mexAB) in hyperoxic condition. Conversely, total ARGs decreased (0.11 ppm) under hypoxic condition marked by a major decline in int1 abundance. Prevalence of global priority pathogens increased in hyperoxic (22.5%), compared to hypoxic (0.9%) wherein major decrease were observed in Pseudomonas, Shigella, and Borrelia. The study observed an increase in superoxide dismutase (sodA, sodB), DNA repair genes (nfo, polA, recA, recB), and ROS (10.4 µmol L[-1]) in adapted biomass with spiked antibiotics. This suggests oxidative damage that facilitates stress-induced mutagenesis providing evidence for observed hyperoxic enrichment of ARGs. Moreover, predominance of catalase (katE, katG) likely limit oxidative damage that deplete ARG breeding in hypoxic condition. The study proposes a link between oxygen levels and AR development that offers insights into mitigation and intervention of AR by controlling oxygen-related stress and strategic selection of bacterial communities.}, }
@article {pmid38000106, year = {2023}, author = {Sidhu, D and Vasundhara, M and Dey, P}, title = {The intestinal-level metabolic benefits of green tea catechins: Mechanistic insights from pre-clinical and clinical studies.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {123}, number = {}, pages = {155207}, doi = {10.1016/j.phymed.2023.155207}, pmid = {38000106}, issn = {1618-095X}, abstract = {BACKGROUND: The intestinal-level host-microbiota interaction has been implicated in the pathogenesis of chronic diseases. The current review is intended to provide a comprehensive insight into deciphering whether intestinal-level bioactivities mediate the overall metabolic health benefits of green tea catechins.<br><br>PURPOSE: We have comprehensively discussed pre-clinical and clinical evidences of intestinal-level changes in metabolism, microbiota, and metabolome due to catechin-rich green tea treatments, ultimately limiting metabolic diseases. Exclusive emphasis has been given to purified catechins and green tea, and discussions on extraintestinal mechanisms of metabolic health benefits were avoided.<br><br>METHODS: A literature search for relevant pre-clinical and clinical studies was performed in various online databases (e.g., PubMed) using specific keywords (e.g., catechin, intestine, microbiota). Out of all the referred literature, &#x223c;15% belonged to 2021-2023, &#x223c;51% were from 2011-2020, and &#x223c;32% from 2000-2010.<br><br>RESULT: The metabolic health benefits of green tea catechins are indeed influenced by the intestinal-level bioactivities, including reduction of mucosal inflammation and oxidative stress, attenuation of gut barrier dysfunction, decrease in intestinal lipid absorption and metabolism, favorable modulation of mucosal nuclear receptor signaling, alterations of the luminal global metabolome, and mitigation of the gut dysbiosis. The results from the recent clinical studies support the pre-clinical evidences. The challenges and pitfalls of the currently available knowledge on catechin bioactivities have been discussed, and constructive directions to harness the translational benefits of green tea through future interventions have been provided.<br><br>CONCLUSION: The metabolism, metabolome, and microbiota at the intestinal epithelia play critical roles in catechin metabolism, pharmacokinetics, bioavailability, and bioactivities. Especially the reciprocal interaction between the catechins and the gut microbiota dictates the metabolic benefits of catechins.}, }
@article {pmid37999520, year = {2023}, author = {Liu, X and Ma, Y and Wu, J and Wang, P and Wang, Y and Wang, A and Yin, Q and Ma, H and Chan, LL and Wu, B}, title = {Characterizing the Influence of a Heterotrophic Bicosoecid Flagellate Pseudobodo sp. on the Dinoflagellate Gambierdiscus balechii.}, journal = {Toxins}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/toxins15110657}, pmid = {37999520}, issn = {2072-6651}, support = {CityU 11104821//General Research Fund of the Hong Kong Research Grants Council/ ; 42176098//National Natural Science Foundation of China/ ; C7013-19GF//Collaborative Research Fund of the Hong Kong Research Grants Council/ ; 2022R52036//The Fund of Special Plan for High-Level Talents of Zhejiang/ ; SGDX20220530111204028//Shenzhen-Hong Kong-Macau Science &amp; Technology Project (Category C)/ ; }, abstract = {Microbial interactions including competition, mutualism, commensalism, parasitism, and predation, which can be triggered by nutrient acquisition and chemical communication, are universal phenomena in the marine ecosystem. The interactions may influence the microbial population density, metabolism, and even their environmental functions. Herein, we investigated the interaction between a heterotrophic bicosoecid flagellate, Pseudobodo sp. (Bicoecea), and a dinoflagellate, Gambierdiscus balechii (Dinophyceae), which is a well-known ciguatera food poisoning (CFP) culprit. The presence of Pseudobodo sp. inhibited the algal proliferation and decreased the cardiotoxicity of zebrafish in the algal extract exposure experiment. Moreover, a significant difference in microbiome abundance was observed in algal cultures with and without Pseudobodo sp. Chemical analysis targeting toxins was performed by using liquid chromatography-tandem mass spectrometry (LC-MS/MS) combined with molecular networking (MN), showing a significant alteration in the cellular production of gambierone analogs and some super-carbon chain compounds. Taken together, our results demonstrated the impact of heterotrophic flagellate on the photosynthetic dinoflagellates, revealing the complex dynamics of algal toxin production and the ecological relationships related to dinoflagellates in the marine environment.}, }
@article {pmid37999473, year = {2023}, author = {Edmunds, CE and Welch, CB and Lourenco, JM and Callaway, TR and Pringle, TD and Dove, CR}, title = {The Effects of Dietary Manganese and Selenium on Growth and the Fecal Microbiota of Nursery Piglets.}, journal = {Veterinary sciences}, volume = {10}, number = {11}, pages = {}, doi = {10.3390/vetsci10110650}, pmid = {37999473}, issn = {2306-7381}, abstract = {The objective of this study was to determine the impact of varying dietary manganese and selenium concentrations, antioxidant cofactors, on the growth performance and fecal microbial populations of nursery pigs. The piglets (N = 120) were blocked by weight (5.22 ± 0.7 kg) and sex. The pens (n = 5/treatment) within a block were randomly assigned to diets in a 2 × 3 factorial design to examine the effects of Se (0.1 and 0.3 mg/kg added Se) and Mn (0, 12, and 24 mg/kg added Mn) and were fed in three phases (P1 = d 1-7, P2 = d 8-21, P3 = d 22-35). The pigs and orts were weighed weekly. Fecal samples were collected d 0 and 35 for 16S rRNA bacterial gene sequencing and VFA analysis. The data were analyzed as factorial via GLM in SAS. There was a linear response (p < 0.05) in overall ADG across dietary Mn. Supplementing 24 mg/kg Mn tended to decrease (p < 0.10) the relative abundance of many bacteria possessing pathogenic traits relative to Mn controls. Meanwhile, increasing Mn concentration tended to foster the growth of bacteria correlated with gut health and improved growth (p < 0.10). The data from this study provide preliminary evidence on the positive effects of manganese on growth and gut health of nursery pigs.}, }
@article {pmid37999467, year = {2023}, author = {Heil, BA and van Heule, M and Thompson, SK and Kearns, TA and Oberhaus, EL and King, G and Daels, P and Dini, P and Sones, JL}, title = {Effect of Sampling Method on Detection of the Equine Uterine Microbiome during Estrus.}, journal = {Veterinary sciences}, volume = {10}, number = {11}, pages = {}, doi = {10.3390/vetsci10110644}, pmid = {37999467}, issn = {2306-7381}, support = {1/CX/CSRD VA/United States ; }, abstract = {Bacterial endometritis is among the most common causes of subfertility in mares. It has a major economic impact on the equine breeding industry. The sensitivity of detecting uterine microbes using culture-based methods, irrespective of the sample collection method, double-guarded endometrial swab, endometrial biopsy, or uterine low-volume lavage (LVL), is low. Therefore, equine bacterial endometritis often goes undiagnosed. Sixteen individual mares were enrolled, and an endometrial sample was obtained using each method from all mares. After trimming, quality control and decontamination, 3824 amplicon sequence variants were detected in the dataset. We found using 16S rRNA sequencing that the equine uterus harbors a distinct resident microbiome during estrus. All three sampling methods used yielded similar results in composition as well as relative abundance at phyla (Proteobacteria, Firmicutes, and Bacteroidota) and genus (Klebsiella, Mycoplasma, and Aeromonas) levels. A significant difference was found in alpha diversity (Chao1) between LVL and endometrial biopsy, suggesting that LVL is superior at detecting the low-abundant (rare) taxa. These new data could pave the way for innovative treatment methods for endometrial disease and subfertility in mares. This, in turn, could lead to more judicious antimicrobial use in the equine breeding industry.}, }
@article {pmid37999464, year = {2023}, author = {Albuquerque, A and Garrido, N and Charneca, R and Egas, C and Martin, L and Ramos, A and Costa, F and Marmelo, C and Martins, JM}, title = {Influence of Sex and a High-Fiber Diet on the Gut Microbiome of Alentejano Pigs Raised to Heavy Weights.}, journal = {Veterinary sciences}, volume = {10}, number = {11}, pages = {}, doi = {10.3390/vetsci10110641}, pmid = {37999464}, issn = {2306-7381}, abstract = {This study investigates the influence of sex and a dietary transition on the gut microbiota of a local Portuguese pig breed. Three groups of male Alentejano pigs (n = 10 each) were raised between ~40 and 160 kg LW. Group C included pigs that were surgically castrated, while the I group included intact ones; both were fed with commercial diets. The third group, IExp, included intact pigs that were fed commercial diets until ~130 kg, then replaced by an experimental diet based on legumes and agro-industrial by-products between ~130 and 160 kg. Fecal samples were collected two weeks before slaughter. The total DNA was extracted and used for 16S metabarcoding on a MiSeq[®] System. The dietary transition from a commercial diet to the experimental diet substantially increased and shifted the diversity observed. Complex carbohydrate fermenting bacteria, such as Ruminococcus spp. and Sphaerochaeta spp., were significantly more abundant in IExp (q < 0.05). On the other hand, castrated pigs presented a significantly lower abundance of the potential probiotic, Roseburia spp. and Lachnospiraceae NK4A136 group (q < 0.01), bacteria commonly associated with better gut health and lower body fat composition. Understanding the role of gut microbiota is paramount to ensure a low skatole deposition and consumers' acceptance of pork products from non-castrated male pigs.}, }
@article {pmid37999433, year = {2023}, author = {Kalabiska, I and Annar, D and Keki, Z and Borbas, Z and Bhattoa, HP and Zsakai, A}, title = {The Oral Microbiome Profile of Water Polo Players Aged 16-20.}, journal = {Sports (Basel, Switzerland)}, volume = {11}, number = {11}, pages = {}, doi = {10.3390/sports11110216}, pmid = {37999433}, issn = {2075-4663}, support = {TEKA grant (EFKTA002T)//Hungarian University of Sports Science/ ; Scientific Foundations of Education Research Program 2021//Hungarian Academy of Sciences/ ; }, abstract = {OBJECTIVES: Chlorine has a strong antibacterial property and is the disinfectant most frequently used in swimming pools. Therefore, the microbiota community in the oral cavity of those who practice water sports is assumed to be special due to their regular immersion in water. Adverse changes in the composition of oral cavity microbiota may have serious health consequences. We aimed to compare the oral microbiome between water polo players and non-athletes. We hypothesized that the oral cavity microbiota community differed between water polo players and non-athletes.<br><br>MATERIALS AND METHODS: Altogether, 124 water polo players (62 males and 62 females, aged between 9 and 20 years) and 16 non-athlete youths (control group, eight males and eight females, aged between 16 and 20 years, mean age + SD = 17.1 + 1.4 years) who participated in body structure examinations voluntarily agreed to participate in the study. In a randomly selected subsample of water polo players (n: 29, aged between 16 and 20 years, mean age + SD = 17.3 + 1.0 years), saliva samples were also collected. Saliva samples were collected from all non-athlete youths (n: 16, aged between 16 and 20 years). The oral microbiome was determined from a saliva sample, and DNA was isolated using the QIAmp DNA Blood Mini Kit. The 16S rRNA gene amplicon sequencing method was used to analyze the microbiome community. PCR primers were trimmed from the sequence reads with Cutadapt. R library DADA2 was used to process reads in the abundance analysis.<br><br>RESULTS: In general, Streptococcus, Veilonella, and Prevotella genera constituted more than 50% of the oral microbiome community in the two participant groups combined (n = 45). The oral microbial profile had significant sexual dimorphism and differed between water polo players and the non-athletes. Compared to females, males had a higher (p < 0.05) relative abundance of the Atopobium (medium effect size) and Pravotella_7 (very large effect size) genera and a lower (p < 0.05) relative abundance of the Fusobacterium (large effect size), Gemella (large effect size), and Streptococcus (large effect size) genera. Compared to non-athletes, water polo players had higher (p < 0.05, medium effect size) relative abundance of the genus Veillonella and lower (p < 0.05, large effect size) relative abundance of the genus Gemella.<br><br>CONCLUSIONS: The results suggest that regular water training can unfavorably alter the composition of the oral microbial community.}, }
@article {pmid37999420, year = {2023}, author = {Oppong-Danquah, E and Blümel, M and Tasdemir, D}, title = {Metabolomics and Microbiomics Insights into Differential Surface Fouling of Three Macroalgal Species of Fucus (Fucales, Phaeophyceae) That Co-Exist in the German Baltic Sea.}, journal = {Marine drugs}, volume = {21}, number = {11}, pages = {}, pmid = {37999420}, issn = {1660-3397}, abstract = {The brown algal genus Fucus provides essential ecosystem services crucial for marine environments. Macroalgae (seaweeds) release dissolved organic matter, hence, are under strong settlement pressure from micro- and macrofoulers. Seaweeds are able to control surface epibionts directly by releasing antimicrobial compounds onto their surfaces, and indirectly by recruiting beneficial microorganisms that produce antimicrobial/antifouling metabolites. In the Kiel Fjord, in the German Baltic Sea, three distinct Fucus species coexist: F. vesiculosus, F. serratus, and F. distichus subsp. evanescens. Despite sharing the same habitat, they show varying fouling levels; F. distichus subsp. evanescens is the least fouled, while F. vesiculosus is the most fouled. The present study explored the surface metabolomes and epiphytic microbiota of these three Fucus spp., aiming to uncover the factors that contribute to the differences in the fouling intensity on their surfaces. Towards this aim, algal surface metabolomes were analyzed using comparative untargeted LC-MS/MS-based metabolomics, to identify the marker metabolites influencing surface fouling. Their epiphytic microbial communities were also comparatively characterized using high-throughput amplicon sequencing, to pinpoint the differences in the surface microbiomes of the algae. Our results show that the surface of the least fouling species, F. distichus subsp. evanescens, is enriched with bioactive compounds, such as betaine lipids MGTA, 4-pyridoxic acid, and ulvaline, which are absent from the other species. Additionally, it exhibits a high abundance of the fungal genera Mucor and Alternaria, along with the bacterial genus Yoonia-Loktanella. These taxa are known for producing antimicrobial/antifouling compounds, suggesting their potential role in the observed fouling resistance on the surface of the F. distichus subsp. evanescens compared to F. serratus and F. vesiculosus. These findings provide valuable clues on the differential surface fouling intensity of Fucus spp., and their importance in marine chemical defense and fouling dynamics.}, }
@article {pmid37999398, year = {2023}, author = {Jahajeeah, D and Ranghoo-Sanmukhiya, M and Schäfer, G}, title = {Metabolic Profiling, Antiviral Activity and the Microbiome of Some Mauritian Soft Corals.}, journal = {Marine drugs}, volume = {21}, number = {11}, pages = {}, pmid = {37999398}, issn = {1660-3397}, support = {WS/MUS22-01//International Centre for Genetic Engineering and Biotechnology/ ; }, abstract = {Soft corals, recognized as sessile marine invertebrates, rely mainly on chemical, rather than physical defense, by secreting intricate secondary metabolites with plausible pharmaceutical implication. Their ecological niche encompasses a diverse community of symbiotic microorganisms which potentially contribute to the biosynthesis of these bioactive metabolites. The emergence of new viruses and heightened viral resistance underscores the urgency to explore novel pharmacological reservoirs. Thus, marine organisms, notably soft corals and their symbionts, have drawn substantial attention. In this study, the chemical composition of four Mauritian soft corals: Sinularia polydactya, Cespitularia simplex, Lobophytum patulum, and Lobophytum crassum was investigated using LC-MS techniques. Concurrently, Illumina 16S metagenomic sequencing was used to identify the associated bacterial communities in the named soft corals. The presence of unique biologically important compounds and vast microbial communities found therein was further followed up to assess their antiviral effects against SARS-CoV-2 and HPV pseudovirus infection. Strikingly, among the studied soft corals, L. patulum displayed an expansive repertoire of unique metabolites alongside a heightened bacterial consort. Moreover, L. patulum extracts exerted some promising antiviral activity against SARS-CoV-2 and HPV pseudovirus infection, and our findings suggest that L. patulum may have the potential to serve as a therapeutic agent in the prevention of infectious diseases, thereby warranting further investigation.}, }
@article {pmid37999261, year = {2023}, author = {Hou, Y and Li, J and Ying, S}, title = {Tryptophan Metabolism and Gut Microbiota: A Novel Regulatory Axis Integrating the Microbiome, Immunity, and Cancer.}, journal = {Metabolites}, volume = {13}, number = {11}, pages = {}, pmid = {37999261}, issn = {2218-1989}, support = {32170062//National Natural Science Foundation of China/ ; 2017TP1037//Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples/ ; }, abstract = {Tryptophan metabolism and gut microbiota form an integrated regulatory axis that impacts immunity, metabolism, and cancer. This review consolidated current knowledge on the bidirectional interactions between microbial tryptophan processing and the host. We focused on how the gut microbiome controls tryptophan breakdown via the indole, kynurenine, and serotonin pathways. Dysbiosis of the gut microbiota induces disruptions in tryptophan catabolism which contribute to disorders like inflammatory conditions, neuropsychiatric diseases, metabolic syndromes, and cancer. These disruptions affect immune homeostasis, neurotransmission, and gut-brain communication. Elucidating the mechanisms of microbial tryptophan modulation could enable novel therapeutic approaches like psychobiotics and microbiome-targeted dietary interventions. Overall, further research on the microbiota-tryptophan axis has the potential to revolutionize personalized diagnostics and treatments for improving human health.}, }
@article {pmid37999254, year = {2023}, author = {Mo, Z and Wang, J and Meng, X and Li, A and Li, Z and Que, W and Wang, T and Tarnue, KF and Ma, X and Liu, Y and Yan, S and Wu, L and Zhang, R and Pei, J and Wang, X}, title = {The Dose-Response Effect of Fluoride Exposure on the Gut Microbiome and Its Functional Pathways in Rats.}, journal = {Metabolites}, volume = {13}, number = {11}, pages = {}, pmid = {37999254}, issn = {2218-1989}, support = {82273749//National Natural Science Foundation of China/ ; 81773468//National Natural Science Foundation of China/ ; LTGY23H240001//Natural Science Foundation of Zhejiang Province, China/ ; NHCKLEE20230908//the Opening Foundation of NHC Key Laboratory of Etiology and Epidemiology/ ; }, abstract = {Metabolic activities within the gut microbiome are intimately linked to human health and disease, especially within the context of environmental exposure and its potential ramifications. Perturbations within this microbiome, termed "gut microbiome perturbations", have emerged as plausible intermediaries in the onset or exacerbation of diseases following environmental chemical exposures, with fluoride being a compound of particular concern. Despite the well-documented adverse impacts of excessive fluoride on various human physiological systems-ranging from skeletal to neurological-the nuanced dynamics between fluoride exposure, the gut microbiome, and the resulting dose-response relationship remains a scientific enigma. Leveraging the precision of 16S rRNA high-throughput sequencing, this study meticulously examines the ramifications of diverse fluoride concentrations on the gut microbiome's composition and functional capabilities within Wistar rats. Our findings indicate a profound shift in the intestinal microbial composition following fluoride exposure, marked by a dose-dependent modulation in the abundance of key genera, including Pelagibacterium, Bilophila, Turicibacter, and Roseburia. Moreover, discernible alterations were observed in critical functional and metabolic pathways of the microbiome, such as D-lyxose ketol-isomerase and DNA polymerase III subunit gamma/tau, underscoring the broad-reaching implications of fluoride exposure. Intriguingly, correlation analyses elucidated strong associations between specific bacterial co-abundance groups (CAGs) and these shifted metabolic pathways. In essence, fluoride exposure not only perturbs the compositional equilibrium of the gut microbiota but also instigates profound shifts in its metabolic landscape. These intricate alterations may provide a mechanistic foundation for understanding fluoride's potential toxicological effects mediated via gut microbiome modulation.}, }
@article {pmid37999221, year = {2023}, author = {Fineide, FA and Tashbayev, B and Elgstøen, KBP and Sandås, EM and Rootwelt, H and Hynne, H and Chen, X and Ræder, S and Vehof, J and Dartt, D and Jensen, JL and Utheim, TP}, title = {Tear and Saliva Metabolomics in Evaporative Dry Eye Disease in Females.}, journal = {Metabolites}, volume = {13}, number = {11}, pages = {}, pmid = {37999221}, issn = {2218-1989}, abstract = {Accurate diagnosis of dry eye disease (DED) is challenging, and even today there is no gold standard biomarker of DED. Hypothesis-free global metabolomic studies of tears from DED patients have great potential to discover metabolites and pathways affected in the pathophysiology of DED, and to identify possible future biomarkers. These metabolites and biomarkers could be important for diagnosing and monitoring disease as well as for new therapeutic targets and strategies. As DED is associated with dry mouth, this study aimed to perform metabolomic analyses of tears and saliva from patients with decreased tear film break-up time but normal Schirmer test, and age-matched controls with both tear production and stability within physiological range. We applied strict inclusion criteria to reduce sampling bias in the metabolomic analyses and selected only age-matched females with Schirmer test values between 10-15 mm/5 min. The tear film analysis arm included 19 patients (with tear film break-up time 0-5 s) and 12 controls (with tear film break-up time 10-30 s), while the salivary analysis arm consisted of a subset which included 18 patients and six controls. Metabolomic analyses were performed using liquid chromatography and high-resolution mass spectrometry. Analyses using a global database search detected a total of 56 metabolites in tear samples that were significantly different between the groups. Of these, several have known associations with DED. These metabolites are present in meibum and have anti-oxidative characteristics or associations with the ocular microbiome, and altered concentrations suggest that they may play a significant role in DED associated with decreased tear film stability. In saliva, hypotaurine levels were lower among patients with tear film instability. In this pilot study, we found different levels of several metabolites in patients with decreased tear film break-up time that may have associations with DED. Future studies are required to replicate our findings and clarify the exact roles of these metabolites.}, }
@article {pmid37999101, year = {2023}, author = {Duttagupta, S and Hakozaki, T and Routy, B and Messaoudene, M}, title = {The Gut Microbiome from a Biomarker to a Novel Therapeutic Strategy for Immunotherapy Response in Patients with Lung Cancer.}, journal = {Current oncology (Toronto, Ont.)}, volume = {30}, number = {11}, pages = {9406-9427}, pmid = {37999101}, issn = {1718-7729}, abstract = {The gastrointestinal microbiome has been shown to play a key role in determining the responses to cancer immunotherapy, including immune checkpoint inhibitor (ICI) therapy and CAR-T. In patients with non-small cell lung cancer (NSCLC), increasing evidence suggests that a microbiome composition signature is associated with clinical response to ICIs as well as with the development of immune-related adverse events. In support of this, antibiotic (ATB)-related dysbiosis has been consistently linked with the deleterious impact of ICI response, shortening the overall survival (OS) among patients on ATBs prior to ICI initiation. In parallel, several preclinical experiments have unravelled various strategies using probiotics, prebiotics, diet, and fecal microbiota transplantation as new therapeutic tools to beneficially shift the microbiome and enhance ICI efficacy. These approaches are currently being evaluated in clinical trials and have achieved encouraging preliminary results. In this article, we reviewed the recent studies on the gut microbiome as a potential biomarker and an adjuvant therapy to ICIs in NSCLC patients.}, }
@article {pmid37999031, year = {2023}, author = {Do, TH and Dao, TK and Nguyen, HD and Truong, NH}, title = {Understanding the Role of Free-Living Bacteria in the Gut of the Lower Termite Coptotermes gestroi Based on Metagenomic DNA Analysis.}, journal = {Insects}, volume = {14}, number = {11}, pages = {}, pmid = {37999031}, issn = {2075-4450}, support = {NVCC08.08/22-23//Vietnam Academy of Sicence and Technology, Vietnam/ ; }, abstract = {Termites' digestive systems, particularly in lower termites with the presence of protozoa, are unique ecological niches that shelter a diverse microbiota with a variety of functions for the host and the environment. In 2012, the metagenomic DNA (5.4 Gb) of the prokaryotes that freely live in the gut of the lower termite Coptotermes gestroi were sequenced. A total of 125,431 genes were predicted and analyzed in order to mine lignocellulolytic genes. however, the overall picture of the structure, diversity, and function of the prokaryotic gut microbiota was not investigated. In the present study, these 125,431 genes were taxonomically classified by MEGAN and functionally annotated by the Kyoto Encyclopedia of Genes and Genomes (KEGG) and by the Carbohydrate-Active enZYmes (CAZy) and HMMER databases. As a result, 95,751 bacterial genes were classified into 35 phyla. The structure of the bacteria, typified by a high ratio of Firmicutes to Bacterioidetes, was distinct from the structure of the entirety of the bacteria in the lower or higher termites' guts. The archaea (533 genes) were distributed into 4 phyla, 10 classes, 15 orders, 21 families, 47 genera, and 61 species. Although freely living in the guts, the prokaryotic community was formed, developed, and adapted to exhibit unique interactions in order to perform mutual roles of benefit to their hosts. Methanobacteriales, accounting for 61% of the archaea symbionts, seem to play an important role in methanogenesis. Concomitantly, bacterial methanotrophs in the gut utilize methane and combine with other bacterial groups, including potential lignocellulolytic degraders, acetogens, sulfur bacteria, and nitrogen-recycling bacteria, to efficiently convert wood with little nitrogen into acetates via certain pathway modules specified by prokaryotes that freely live in the gut. This forms an important energy source for the termites. Furthermore, bacteria carry 2223 genes involved in the biosynthesis of 17 antibiotic groups. The gut bacteria also possess genes for the degradation of 18 toxic aromatic compounds, of which four are commercial pesticides against termites commonly used for the preservation of wooden constructions. Eight of the eighteen pathways were the first to be reported from the termite gut. Overall, this study sheds light on the roles of the freely living bacteria and archaea in the C. gestroi gut, providing evidence that the gut microbiome acts as the second host genome, contributing both nutrients and immunity to support the host's existence, growth, and development.}, }
@article {pmid37998924, year = {2023}, author = {Theologidis, I and Karamitros, T and Vichou, AE and Kizis, D}, title = {Nanopore-Sequencing Metabarcoding for Identification of Phytopathogenic and Endophytic Fungi in Olive (Olea europaea) Twigs.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {11}, pages = {}, pmid = {37998924}, issn = {2309-608X}, support = {Olive Roads//GSRI/ ; }, abstract = {Metabarcoding approaches for the identification of plant disease pathogens and characterization of plant microbial populations constitute a rapidly evolving research field. Fungal plant diseases are of major phytopathological concern; thus, the development of metabarcoding approaches for the detection of phytopathogenic fungi is becoming increasingly imperative in the context of plant disease prognosis. We developed a multiplex metabarcoding method for the identification of fungal phytopathogens and endophytes in olive young shoots, using the MinION sequencing platform (Oxford Nanopore Technologies). Selected fungal-specific primers were used to amplify three different genomic DNA loci (ITS, beta-tubulin, and 28S LSU) originating from olive twigs. A multiplex metabarcoding approach was initially evaluated using healthy olive twigs, and further assessed with naturally infected olive twig samples. Bioinformatic analysis of basecalled reads was carried out using MinKNOW, BLAST+ and R programming, and results were also evaluated using the BugSeq cloud platform. Data analysis highlighted the approaches based on ITS and their combination with beta-tubulin as the most informative ones according to diversity estimations. Subsequent implementation of the method on symptomatic samples identified major olive pathogens and endophytes including genera such as Cladosporium, Didymosphaeria, Paraconiothyrium, Penicillium, Phoma, Verticillium, and others.}, }
@article {pmid37998910, year = {2023}, author = {Carlson, SL and Mathew, L and Savage, M and Kok, K and Lindsay, JO and Munro, CA and McCarthy, NE}, title = {Mucosal Immunity to Gut Fungi in Health and Inflammatory Bowel Disease.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {11}, pages = {}, pmid = {37998910}, issn = {2309-608X}, abstract = {The gut microbiome is a diverse microbial community composed of bacteria, viruses, and fungi that plays a major role in human health and disease. Dysregulation of these gut organisms in a genetically susceptible host is fundamental to the pathogenesis of inflammatory bowel disease (IBD). While bacterial dysbiosis has been a predominant focus of research for many years, there is growing recognition that fungal interactions with the host immune system are an important driver of gut inflammation. Candida albicans is likely the most studied fungus in the context of IBD, being a near universal gut commensal in humans and also a major barrier-invasive pathogen. There is emerging evidence that intra-strain variation in C. albicans virulence factors exerts a critical influence on IBD pathophysiology. In this review, we describe the immunological impacts of variations in C. lbicans colonisation, morphology, genetics, and proteomics in IBD, as well as the clinical and therapeutic implications.}, }
@article {pmid37998819, year = {2023}, author = {DuPont, HL and Salge, MMH}, title = {The Importance of a Healthy Microbiome in Pregnancy and Infancy and Microbiota Treatment to Reverse Dysbiosis for Improved Health.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {11}, pages = {}, pmid = {37998819}, issn = {2079-6382}, abstract = {BACKGROUND: The microbiome of newborn infants during the first 1000 days, influenced early on by their mothers' microbiome health, mode of delivery and breast feeding, orchestrates the education and programming of the infant's immune system and determines in large part the general health of the infant for years.<br><br>METHODS: PubMed was reviewed for maternal infant microbiome health and microbiota therapy in this setting with prebiotics, probiotics, vaginal seeding and fecal microbiota transplantation (FMT).<br><br>RESULTS: A healthy nonobese mother, vaginal delivery and strict breast feeding contribute to microbiome health in a newborn and young infant. With reduced microbiome diversity (dysbiosis) during pregnancy, cesarean delivery, prematurity, and formula feeding contribute to dysbiosis in the newborn. Microbiota therapy is an important approach to repair dysbiosis in pregnant women and their infants. Currently available probiotics can have favorable metabolic effects on mothers and infants, but these effects are variable. In research settings, reversal of infant dysbiosis can be achieved via vaginal seeding or FMT. Next generation probiotics in development should replace current probiotics and FMT.<br><br>CONCLUSIONS: The most critical phase of human microbiome development is in the first 2-3 years of life. Preventing and treating dysbiosis during pregnancy and early life can have a profound effect on an infant's later health.}, }
@article {pmid37998812, year = {2023}, author = {Chun Giok, K and Menon, RK}, title = {The Microbiome of Peri-Implantitis: A Systematic Review of Next-Generation Sequencing Studies.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {11}, pages = {}, pmid = {37998812}, issn = {2079-6382}, support = {//Ajman University/ ; }, abstract = {(1) Introduction: Current evidence shows that mechanical debridement augmented with systemic and topical antibiotics may be beneficial for the treatment of peri-implantitis. The microbial profile of peri-implantitis plays a key role in identifying the most suitable antibiotics to be used for the treatment and prevention of peri-implantitis. This systematic review aimed to summarize and critically analyze the methodology and findings of studies which have utilized sequencing techniques to elucidate the microbial profiles of peri-implantitis. (2) Results: Fusobacterium, Treponema, and Porphyromonas sp. are associated with peri-implantitis. Veillonella sp. are associated with healthy implant sites and exhibit a reduced prevalence in deeper pockets and with greater severity of disease progression. Streptococcus sp. have been identified both in diseased and healthy sites. Neisseria sp. have been associated with healthy implants and negatively correlate with the probing depth. Methanogens and AAGPRs were also detected in peri-implantitis sites. (3) Methods: The study was registered with the International Prospective Register of Systematic Reviews (PROSPERO) (CRD42023459266). The PRISMA criteria were used to select articles retrieved from a systematic search of the Scopus, Cochrane, and Medline databases until 1 August 2023. Title and abstract screening was followed by a full-text review of the included articles. Thirty-two articles were included in the final qualitative analysis. (4) Conclusions: A distinct microbial profile could not be identified from studies employing sequencing techniques to identify the microbiome. Further studies are needed with more standardization to allow a comparison of findings. A universal clinical parameter for the diagnosis of peri-implantitis should be implemented in all future studies to minimize confounding factors. The subject pool should also be more diverse and larger to compensate for individual differences, and perhaps a distinct microbial profile can be seen with a larger sample size.}, }
@article {pmid37998808, year = {2023}, author = {Thavamani, A and Sankararaman, S and Al-Shakhshir, H and Retuerto, M and Velayuthan, S and Sferra, TJ and Ghannoum, M}, title = {Impact of Erythromycin as a Prokinetic on the Gut Microbiome in Children with Feeding Intolerance-A Pilot Study.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {11}, pages = {}, pmid = {37998808}, issn = {2079-6382}, support = {Rainbow Children's Foundation, Cleveland//Rainbow Children's Foundation, Cleveland/ ; AI145289//National Institutes of Health grant to Mahmoud Ghannoum./ ; }, abstract = {BACKGROUND: Studies have demonstrated that the gut microbiome changes upon exposure to systemic antibiotics. There is a paucity of literature regarding impact on the gut microbiome by long-term usage of erythromycin ethyl succinate (EES) when utilized as a prokinetic.<br><br>METHODS: Stool samples from pediatric patients with feeding intolerance who received EES (N = 8) as a prokinetic were analyzed for both bacteriome and mycobiome. Age-matched children with similar clinical characteristics but without EES therapy were included as controls (N = 20).<br><br>RESULTS: In both groups, Proteobacteria, Firmicutes, and Bacteroidetes were the most abundant bacterial phyla. Ascomycota was the most abundant fungal phyla, followed by Basidiomycota. There were no significant differences in richness between the groups for both bacterial and fungal microbiome. Alpha diversity (at genus and species levels) and beta diversity (at the genus level) were not significantly different between the groups for both bacterial and fungal microbiome. At the species level, there was a significant difference between the groups for fungal microbiota, with a p-value of 0.029. We also noted that many fungal microorganisms had significantly higher p-values in the EES group than controls at both genera and species levels.<br><br>CONCLUSIONS: In this observational case-control study, the prokinetic use of EES was associated with changes in beta diversity between the groups for mycobiome at the species level. Many fungal microorganisms were significantly higher in the EES group when compared to the controls. Confirmation of these results in larger trials will provide further evidence regarding the impact of EES on gut microbiota when utilized as a prokinetic agent.}, }
@article {pmid37998794, year = {2023}, author = {Akomoneh, EA and Gestels, Z and Abdellati, S and Vereecken, K and Bartholomeeusen, K and Van den Bossche, D and Kenyon, C and Manoharan-Basil, SS}, title = {Genome Mining Uncovers NRPS and PKS Clusters in Rothia dentocariosa with Inhibitory Activity against Neisseria Species.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {11}, pages = {}, pmid = {37998794}, issn = {2079-6382}, support = {2021//SOFI 2021 grant/ ; }, abstract = {The growing global threat of antimicrobial resistance is reaching a crisis point as common bacterial infections, including those caused by pathogenic Neisseria species, are becoming increasingly untreatable. This is compelling the scientific community to search for new antimicrobial agents, taking advantage of computational mining and using whole genome sequences to discover natural products from the human microbiome with antibiotic effects. In this study, we investigated the crude extract from a Rothia dentocariosa strain with demonstrated antimicrobial activity against pathogenic Neisseria spp. by spot-on-lawn assay. The genomic DNA of the R. dentocariosa strain was sequenced, and bioinformatic evaluation was performed using antiSMASH and PRISM to search for biosynthetic gene clusters (BGCs). The crude extract with potential antimicrobial activity was run on Tricine-SDS-PAGE, and the putative peptides were characterised using liquid chromatography-tandem mass spectrometry (LC-MS). The crude extract inhibited the growth of the pathogenic Neisseria spp. Six BGCs were identified corresponding to non-ribosomal peptide synthases (NRPSs), polyketide synthases (PKSs), and ribosomally synthesised and post-translationally modified peptides. Three peptides were also identified corresponding to Actinorhodin polyketide putative beta-ketoacyl synthase 1. These findings serve as a useful reference to facilitate the research and development of NRPS and PKS as antimicrobial products against multidrug-resistant N. gonorrhoeae.}, }
@article {pmid37998359, year = {2023}, author = {Bosveld, CJ and Guth, C and Limjunyawong, N and Pundir, P}, title = {Emerging Role of the Mast Cell-Microbiota Crosstalk in Cutaneous Homeostasis and Immunity.}, journal = {Cells}, volume = {12}, number = {22}, pages = {}, pmid = {37998359}, issn = {2073-4409}, support = {NSERC RGPIN-2022-03453//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {The skin presents a multifaceted microbiome, a balanced coexistence of bacteria, fungi, and viruses. These resident microorganisms are fundamental in upholding skin health by both countering detrimental pathogens and working in tandem with the skin's immunity. Disruptions in this balance, known as dysbiosis, can lead to disorders like psoriasis and atopic dermatitis. Central to the skin's defense system are mast cells. These are strategically positioned within the skin layers, primed for rapid response to any potential foreign threats. Recent investigations have started to unravel the complex interplay between these mast cells and the diverse entities within the skin's microbiome. This relationship, especially during times of both balance and imbalance, is proving to be more integral to skin health than previously recognized. In this review, we illuminate the latest findings on the ties between mast cells and commensal skin microorganisms, shedding light on their combined effects on skin health and maladies.}, }
@article {pmid37998334, year = {2023}, author = {Newman, TM and Wilson, AS and Clear, KYJ and Tallant, EA and Gallagher, PE and Cook, KL}, title = {Probiotic and Muscadine Grape Extract Interventions Shift the Gut Microbiome and Improve Metabolic Parameters in Female C57BL/6 Mice.}, journal = {Cells}, volume = {12}, number = {22}, pages = {}, pmid = {37998334}, issn = {2073-4409}, support = {T32CA247819/CA/NCI NIH HHS/United States ; P30CA012197/CA/NCI NIH HHS/United States ; }, abstract = {Obesity and Western-like diet consumption leads to gut microbiome dysbiosis, which is associated with the development of cardio-metabolic diseases and poor health outcomes. The objective of this study was to reduce Western diet-mediated gut microbial dysbiosis, metabolic dysfunction, and systemic inflammation through the administration of a novel combined intervention strategy (oral probiotic bacteria supplements and muscadine grape extract (MGE)). To do so, adult female C57BL/6 mice were fed a low-fat control or Western-style diet and sub-grouped into diet alone, probiotic intervention, antibiotic treatments, MGE supplementation, a combination of MGE and probiotics, or MGE and antibiotics for 13 weeks. Mouse body weight, visceral adipose tissue (VAT), liver, and mammary glands (MG) were weighed at the end of the study. Fecal 16S rRNA sequencing was performed to determine gut bacterial microbiome populations. Collagen, macrophage, and monocyte chemoattractant protein-1 (MCP-1) in the VAT and MG tissue were examined by immunohistochemistry. Adipocyte diameter was measured in VAT. Immunohistochemistry of intestinal segments was used to examine villi length, muscularis thickness, and goblet cell numbers. We show that dietary interventions in Western diet-fed mice modulated % body weight gain, visceral adiposity, MG weight, gut microbial populations, and inflammation. Intervention strategies in both diets effectively reduced VAT and MG fibrosis, VAT and MG macrophages, adipocyte diameter, and VAT and MG MCP-1. Interventions also improved intestinal health parameters. In conclusion, dietary intervention with MGE and probiotics modulates several microbial, inflammatory, and metabolic factors reducing poor health outcomes associated with Western diet intake.}, }
@article {pmid37998032, year = {2023}, author = {Li, X and Yang, L and Jiang, S and Zhou, F and Jiang, S and Li, Y and Chen, X and Yang, Q and Duan, Y and Huang, J}, title = {Effect of Fly Maggot Protein as Dietary on Growth and Intestinal Microbial Community of Pacific White Shrimp Litopenaeus vannamei.}, journal = {Biology}, volume = {12}, number = {11}, pages = {}, pmid = {37998032}, issn = {2079-7737}, support = {2022YFD2400104, 2022SPY02001&#xff0c;2022SPY00002&#xff0c;2022SJS02001, CARS-48, CAFS (NO.2023TD34)//National Key R &amp; D Program of China (2022YFD2400104), Rural Revitalization Strategy Special Fund Seed Industry Revitalization Project of Guangdong Province (2022SPY02001&#xff0c;2022SPY00002&#xff0c;2022SJS02001), China Agriculture Research System of MOF and MARA(CARS-48/ ; }, abstract = {As the intensive development of aquaculture persists, the demand for fishmeal continues to grow; however, since fishery resources are limited, the price of fishmeal remains high. Therefore, there is an urgent need to develop new sources of protein. They are rich in proteins, fatty acids, amino acids, chitin, vitamins, minerals, and antibacterial substances. Maggot meal-based diet is an ideal source of high-quality animal protein and a new type of protein-based immune enhancer with good application prospects in animal husbandry and aquaculture. In the present study, we investigated the effects of three different diets containing maggot protein on the growth and intestinal microflora of Litopenaeus vannamei. The shrimp were fed either a control feed (no fly maggot protein added), FM feed (compound feed with 30% fresh fly maggot protein added), FF feed (fermented fly maggot protein), or HT feed (high-temperature pelleted fly maggot protein) for eight weeks. The results showed that fresh fly maggot protein in the feed was detrimental to shrimp growth, whereas fermented and high-temperature-pelleted fly maggot protein improved shrimp growth and survival. The effects of different fly maggot protein treatments on the intestinal microbiota of L. vannamei also varied. Fermented fly maggot protein feed and high-temperature-pelleted fly maggot protein feed increased the relative abundance of Ruegeria and Pseudomonas, which increased the abundance of beneficial bacteria and thus inhibited the growth of harmful bacteria. In contrast, fresh fly maggot proteins alter the intestinal microbiome, disrupting symbiotic relationships between bacteria, and causing invasion by Vibrio and antibiotic-resistant bacteria. These results suggest that fresh fly maggot proteins affect the composition of intestinal microorganisms, which is detrimental to the intestinal tract of L. vannamei, whereas fermented fly maggot protein feed affected the growth of L. vannamei positively by improving the composition of intestinal microorganisms.}, }
@article {pmid37998019, year = {2023}, author = {Goraj, W and Pytlak, A and Grządziel, J and Gałązka, A and Stępniewska, Z and Szafranek-Nakonieczna, A}, title = {Dynamics of Methane-Consuming Biomes from Wieliczka Formation: Environmental and Enrichment Studies.}, journal = {Biology}, volume = {12}, number = {11}, pages = {}, pmid = {37998019}, issn = {2079-7737}, support = {DEC-2014/15/N/NZ8/00315//National Science Center/ ; }, abstract = {The rocks surrounding Wieliczka salt deposits are an extreme, deep subsurface ecosystem that as we studied previously harbors many microorganisms, including methanotrophs. In the presented research bacterial community structure of the Wieliczka Salt Mine was determined as well as the methanotrophic activity of the natural microbiome. Finally, an enrichment culture of methane-consuming methanotrophs was obtained. The research material used in this study consisted of rocks surrounding salt deposits in the Wieliczka Salt Mine. DNA was extracted directly from the pristine rock material, as well as from rocks incubated in an atmosphere containing methane and mineral medium, and from a methanotrophic enrichment culture from this ecosystem. As a result, the study describes the composition of the microbiome in the rocks surrounding the salt deposits, while also explaining how biodiversity changes during the enrichment culture of the methanotrophic bacterial community. The contribution of methanotrophic bacteria ranged from 2.614% in the environmental sample to 64.696% in the bacterial culture. The methanotrophic enrichment culture was predominantly composed of methanotrophs from the genera Methylomonas (48.848%) and Methylomicrobium (15.636%) with methane oxidation rates from 3.353 ± 0.105 to 4.200 ± 0.505 µmol CH4 mL[-1] day[-1].}, }
@article {pmid37997962, year = {2023}, author = {Yang, L and Wan, X and Zhou, R and Yuan, Y}, title = {The Composition and Function of the Rhizosphere Bacterial Community of Paeonia lactiflora Varies with the Cultivar.}, journal = {Biology}, volume = {12}, number = {11}, pages = {}, pmid = {37997962}, issn = {2079-7737}, abstract = {The composition and diversity of the rhizosphere microbial community maintain the stability of the root microclimate, and several studies have focused on this aspect of rhizosphere microorganisms. However, how these communities vary with cultivars of a species is not completely understood. Paeonia lactiflora-a perennial herb species of the family Paeoniaceae-includes a wide variety of cultivars, with rich rhizosphere microbial resources. Hence, we studied the differences in rhizosphere bacterial communities associated with eight P. lactiflora cultivars. We noted that Actinobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, Planctomycetes and Chloroflexi were the dominant phyla associated with the cultivars. The composition of rhizosphere bacterial community of different cultivars was highly similar at taxonomic levels, but there were slightly differences in the relative abundance. LEfSe analysis showed that the cultivars "Sheng Tao Hua" and "Zi Lou Xian Jin" exhibited the most biomarkers. Differential ASV analysis revealed the maximum difference in ASV abundance between "Lian Tai" and "Zi Hong Zheng Hui", as well as between "Sheng Tao Hua" and "Tao Hua Fei Xue", and the maximum similarity between "Duo Ye Zi" and "Xue Feng". Co-occurrence network analysis revealed that rhizosphere bacteria in most cultivars maintain homeostasis by cooperation, wherein Actinobacteria and Proteobacteria played a vital role. In addition, microbial resources related to cultivars like bioremediation, organic degradation and resistance to diseases are found. This study revealed the structures of the rhizosphere bacterial communities associated with different cultivars of P. lactiflora and explored their stress resistance potential, which can be used to guide future agricultural practices.}, }
@article {pmid37997887, year = {2023}, author = {Png, LH and Ng, DHL and Teo, NWY}, title = {Infectious disease for the rhinologist.}, journal = {Current opinion in otolaryngology &amp; head and neck surgery}, volume = {}, number = {}, pages = {}, pmid = {37997887}, issn = {1531-6998}, abstract = {PURPOSE OF REVIEW: The purpose of this review is to summarize the recent literature relating to viral, fungal and bacterial infections and their interactions within the sinonasal tract in the past 18 months.<br><br>RECENT FINDINGS: Coronavirus disease 2019 (COVID-19)-associated olfactory dysfunction (OD) is variant dependent. Magnetic resonance imaging studies have found greater olfactory cleft opacification and higher olfactory bulb volume in post-COVID-19 OD. Olfactory training remains the mainstay of treatment, while platelet-rich plasma injections and ultramicronized palmitoylethanolamide and luteolin combination oral supplementation have shown early promise.Consensus statements on paranasal sinus fungal balls and acute invasive fungal sinusitis have been released.Studies on the nasal microbiome have reported Staphylococcus and Corynebacterium as the most abundant genera, with higher levels of Staphylococcus and Corynebacterium being found in patients with chronic rhinosinusitis (CRS) and healthy individuals respectively. However, there is conflicting evidence on the significance of biodiversity of the nasal microbiome found in CRS versus healthy patients.<br><br>SUMMARY: While the peak of the COVID-19 pandemic is behind us, its sequelae continue to pose treatment challenges. Further studies in OD have implications in managing the condition, beyond those afflicted post-COVID-19 infection. Similarly, more research is needed in studying the nasal microbiome and its implications in the development and treatment of CRS.}, }
@article {pmid37997859, year = {2023}, author = {Cox, A and Bomstein, Z and Jayaraman, A and Allred, C}, title = {The intestinal microbiota as mediators between dietary contaminants and host health.}, journal = {Experimental biology and medicine (Maywood, N.J.)}, volume = {}, number = {}, pages = {15353702231208486}, doi = {10.1177/15353702231208486}, pmid = {37997859}, issn = {1535-3699}, abstract = {The gut microbiota sit at an important interface between the host and the environment, and are exposed to a multitude of nutritive and non-nutritive substances. These microbiota are critical to maintaining host health, but their supportive roles may be compromised in response to endogenous compounds. Numerous non-nutritive substances are introduced through contaminated foods, with three common groups of contaminants being bisphenols, phthalates, and mycotoxins. The former contaminants are commonly introduced through food and/or beverages packaged in plastic, while mycotoxins contaminate various crops used to feed livestock and humans alike. Each group of contaminants have been shown to shift microbial communities following exposure; however, specific patterns in microbial responses have yet to be identified, and little is known about the capacity of the microbiota to metabolize these contaminants. This review characterizes the state of existing research related to gut microbial responses to and biotransformation of bisphenols, phthalates, and mycotoxins. Collectively, we highlight the need to identify consistent, contaminant-specific responses in microbial shifts, whether these community alterations are a result of contaminant effects on the host or microbiota directly, and to identify the extent of contaminant biotransformation by microbiota, including if these transformations occur in physiologically relevant contexts.}, }
@article {pmid37997816, year = {2024}, author = {Kumavath, R and Pavithran, H and Paul, S and Anju, VT and Busi, S and Dyavaiah, M}, title = {Effects of gut microbiome and obesity on the development, progression and prevention of cancer (Review).}, journal = {International journal of oncology}, volume = {64}, number = {1}, pages = {}, doi = {10.3892/ijo.2023.5592}, pmid = {37997816}, issn = {1791-2423}, abstract = {Cancer is one of the leading causes of death worldwide and it is estimated that the mortality rate of cancer will increase in the coming years. The etiology of the development and progression of cancer is multifactorial. Insights have been gained on the association between the human microbiome and tumor cell malignancy. A number of commensal microbe species are present in the human gut. They serve pivotal roles in maintaining several health and disease conditions, such as inflammatory bowel disease, irritable bowel syndrome, obesity and diabetes. Known major factors involved in cancer development include age, hormone levels, alcohol consumption, diet, being overweight, obesity, and infections, regardless of the type of cancer. Therefore, the present review aims to discuss the relationship between the gut microbiome and obesity‑associated malignancies, including colorectal, gastric and liver cancer. Obesity has been reported to contribute to the development of numerous types of cancer primarily caused by high fatty food intake. In addition, obesity‑associated microbiome alterations can lead to cancer and its progression. Dysbiosis of the gut microbiota can alter the metabolite profile, whilst increasing the levels of toxins, such as Bacteroides fragilis toxin and colibactin and cytolethal distending toxin, which are responsible for oncogenesis. The present review provides insights into the impact of gut microbiome dysbiosis on the progression of different types of cancers associated with obesity. It also discusses possible strategies for preserving a healthy gut microbiome. Different pre‑clinical and clinical models are available for studying cancer development downstream of gut microbiome dysbiosis. Furthermore, the role of metabolites or drugs employed in colorectal, gastric and liver cancer therapy would be discussed.}, }
@article {pmid37997753, year = {2023}, author = {Oldereid, TS and Jiang, X and Øgaard, J and Schrumpf, E and Bjørnholt, JV and Rasmussen, H and Melum, E}, title = {Microbial exposure during early life regulates development of bile duct inflammation.}, journal = {Scandinavian journal of gastroenterology}, volume = {}, number = {}, pages = {1-10}, doi = {10.1080/00365521.2023.2278423}, pmid = {37997753}, issn = {1502-7708}, abstract = {OBJECTIVES: The early life microbiome has been linked to inflammatory diseases in adulthood and a role for the microbiome in bile duct inflammation is supported by both human and murine studies. We utilized the NOD.c3c4 mouse model that develops a spontaneous immune-driven biliary disease with a known contribution of the microbiome to evaluate the temporal effects of the early life microbiome.<br><br>MATERIALS AND METHODS: Germ-free (GF) NOD.c3c4 mice were conventionalized into a specific pathogen free environment at birth (conventionally raised, CONV-R) or at weaning (germ-free raised, GF-R) and compared with age and gender-matched GF and conventional (CONV) NOD.c3c4 mice. At 9&#x2009;weeks of age, liver pathology was assessed by conventional histology and flow cytometry immunophenotyping.<br><br>RESULTS: Neonatal exposure to microbes (CONV-R) increased biliary inflammation to similar levels as regular conventional NOD.c3c4 mice, while delayed exposure to microbes (GF-R) restrained the biliary inflammation. Neutrophil infiltration was increased in all conventionalized mice compared to GF. An immunophenotype in the liver similar to CONV was restored in both CONV-R and GF-R compared to GF mice displaying a proportional increase of B cells and reduction of T cells in the liver.<br><br>CONCLUSIONS: Microbial exposure during early life has a temporal impact on biliary tract inflammation in the NOD.c3c4 mouse model suggesting that age-sensitive interaction with commensal microbes have long-lasting effects on biliary immunity that can be of importance for human cholangiopathies.}, }
@article {pmid37997472, year = {2023}, author = {Akbari, E and Milani, A and Seyedinkhorasani, M and Bolhassani, A}, title = {HPV co-infections with other pathogens in cancer development: A comprehensive review.}, journal = {Journal of medical virology}, volume = {95}, number = {11}, pages = {e29236}, doi = {10.1002/jmv.29236}, pmid = {37997472}, issn = {1096-9071}, abstract = {High-risk human papillomaviruses (HR-HPVs) cause various malignancies in the anogenital and oropharyngeal regions. About 70% of cervical and oropharyngeal cancers are caused by HPV types 16 and 18. Notably, some viruses including herpes simplex virus, Epstein-Barr virus, and human immunodeficiency virus along with various bacteria often interact with HPV, potentially impacting its replication, persistence, and cancer progression. Thus, HPV infection can be significantly influenced by co-infecting agents that influence infection dynamics and disease progression. Bacterial co-infections (e.g., Chlamydia trachomatis) along with bacterial vaginosis-related species also interact with HPV in genital tract leading to viral persistence and disease outcomes. Co-infections involving HPV and diverse infectious agents have significant implications for disease transmission and clinical progression. This review explores multiple facets of HPV infection encompassing the co-infection dynamics with other pathogens, interaction with the human microbiome, and its role in disease development.}, }
@article {pmid37996960, year = {2023}, author = {Gafen, HB and Liu, CC and Ineck, NE and Scully, CM and Mironovich, MA and Taylor, CM and Luo, M and Leis, ML and Scott, EM and Carter, RT and Hernke, DM and Paul, NC and Lewin, AC}, title = {Alterations to the bovine bacterial ocular surface microbiome in the context of infectious bovine keratoconjunctivitis.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {60}, pmid = {37996960}, issn = {2524-4671}, support = {12897461//USDA AFRI/ ; }, abstract = {BACKGROUND: Infectious bovine keratoconjunctivitis (IBK) is a common cause of morbidity in cattle, resulting in significant economic losses. This study aimed to characterize the bovine bacterial ocular surface microbiome (OSM) through conjunctival swab samples from Normal eyes and eyes with naturally acquired, active IBK across populations of cattle using a three-part approach, including bacterial culture, relative abundance (RA, 16 S rRNA gene sequencing), and semi-quantitative random forest modeling (real-time polymerase chain reaction (RT-PCR)).<br><br>RESULTS: Conjunctival swab samples were obtained from eyes individually classified as Normal (n&#x2009;=&#x2009;376) or IBK (n&#x2009;=&#x2009;228) based on clinical signs. Cattle unaffected by IBK and the unaffected eye in cattle with contralateral IBK were used to obtain Normal eye samples. Moraxella bovis was cultured from similar proportions of IBK (7/228, 3.07%) and Normal eyes (1/159, 0.63%) (p&#x2009;=&#x2009;0.1481). Moraxella bovoculi was cultured more frequently (p&#x2009;<&#x2009;0.0001) in IBK (59/228, 25.88%) than Normal (7/159, 4.40%) eyes. RA (via 16&#xa0;S rRNA gene sequencing) of Actinobacteriota was significantly higher in Normal eyes (p&#x2009;=&#x2009;0.0045). Corynebacterium variabile and Corynebacterium stationis (Actinobacteriota) were detected at significantly higher RA (p&#x2009;=&#x2009;0.0008, p&#x2009;=&#x2009;0.0025 respectively) in Normal eyes. Rothia nasimurium (Actinobacteriota) was detected at significantly higher RA in IBK eyes (p&#x2009;<&#x2009;0.0001). Alpha-diversity index was not significantly different between IBK and Normal eyes (p&#x2009;>&#x2009;0.05). Alpha-diversity indices for geographic location (p&#x2009;<&#x2009;0.001), age (p&#x2009;<&#x2009;0.0001), sex (p&#x2009;<&#x2009;0.05) and breed (p&#x2009;<&#x2009;0.01) and beta-diversity indices for geographic location (p&#x2009;<&#x2009;0.001), disease status (p&#x2009;<&#x2009;0.01), age (p&#x2009;<&#x2009;0.001), sex (p&#x2009;<&#x2009;0.001) and breed (p&#x2009;<&#x2009;0.001) were significantly different between groups. Modeling of RT-PCR values reliably categorized the microbiome of IBK and Normal eyes; primers for Moraxella bovoculi, Moraxella bovis, and Staphylococcus spp. were consistently the most significant canonical variables in these models.<br><br>CONCLUSIONS: The results provide further evidence that multiple elements of the bovine bacterial OSM are altered in the context of IBK, indicating the involvement of a variety of bacteria in addition to Moraxella bovis, including Moraxella bovoculi and R. nasimurium, among others. Actinobacteriota RA is altered in IBK, providing possible opportunities for novel therapeutic interventions. While RT-PCR modeling provided limited further support for the involvement of Moraxella bovis in IBK, this was not overtly reflected in culture or RA results. Results also highlight the influence of geographic location and breed type (dairy or beef) on the bovine bacterial OSM. RT-PCR modeling reliably categorized samples as IBK or Normal.}, }
@article {pmid37996910, year = {2023}, author = {Li, J and Zou, Y and Li, Q and Zhang, J and Bourne, DG and Lyu, Y and Liu, C and Zhang, S}, title = {A coral-associated actinobacterium mitigates coral bleaching under heat stress.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {83}, pmid = {37996910}, issn = {2524-6372}, support = {42122045//National Natural Science Foundation of China/ ; 41890853//National Natural Science Foundation of China/ ; GJTD-2020-12//K. C. Wong Education Foundation/ ; }, abstract = {BACKGROUND: The positive effects of exposing corals to microorganisms have been reported though how the benefits are conferred are poorly understood. Here, we isolated an actinobacterial strain (SCSIO 13291) from Pocillopora damicornis with capabilities to synthesize antioxidants, vitamins, and antibacterial and antiviral compounds supported with phenotypic and/or genomic evidence. Strain SCSIO 13291 was labeled with 5 (and - 6)-carboxytetramethylrhodamine, succinimidyl ester and the labeled cell suspension directly inoculated onto the coral polyp tissues when nubbins were under thermal stress in a mesocosm experiment. We then visualized the labelled bacterial cells and analyzed the coral physiological, transcriptome and microbiome to elucidate the effect this strain conferred on the coral holobiont under thermal stress.<br><br>RESULTS: Subsequent microscopic observations confirmed the presence of the bacterium attached to the coral polyps. Addition of the SCSIO 13291 strain reduced signs of bleaching in the corals subjected to heat stress. At the same time, alterations in gene expression, which were involved in reactive oxygen species and light damage mitigation, attenuated apoptosis and exocytosis in addition to metabolite utilization, were observed in the coral host and Symbiodiniaceae populations. In addition, the coral associated bacterial community altered with a more stable ecological network for samples inoculated with the bacterial strain.<br><br>CONCLUSIONS: Our results provide insights into the benefits of a putative actinobacterial probiotic strain that mitigate coral bleaching signs. This study suggests that the inoculation of bacteria can potentially directly benefit the coral holobiont through conferring metabolic activities or through indirect mechanisms of suppling additional nutrient sources.}, }
@article {pmid37996903, year = {2023}, author = {Swift, JF and Migicovsky, Z and Trello, GE and Miller, AJ}, title = {Grapevine bacterial communities display compartment-specific dynamics over space and time within the Central Valley of California.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {84}, pmid = {37996903}, issn = {2524-6372}, support = {1546869//National Science Foundation Plant Genome Research Program/ ; 1758713//National Science Foundation Graduate Research Fellowship/ ; }, abstract = {BACKGROUND: Plant organs (compartments) host distinct microbiota which shift in response to variation in both development and climate. Grapevines are woody perennial crops that are clonally propagated and cultivated across vast geographic areas, and as such, their microbial communities may also reflect site-specific influences. These site-specific influences along with microbial differences across sites compose 'terroir', the environmental influence on wine produced in a given region. Commercial grapevines are typically composed of a genetically distinct root (rootstock) grafted to a shoot system (scion) which adds an additional layer of complexity via genome-to-genome interactions.<br><br>RESULTS: To understand spatial and temporal patterns of bacterial diversity in grafted grapevines, we used 16S rRNA amplicon sequencing to quantify soil and compartment microbiota (berries, leaves, and roots) for grafted grapevines in commercial vineyards across three counties in the Central Valley of California over two successive growing seasons. Community composition revealed compartment-specific dynamics. Roots assembled site-specific bacterial communities that reflected rootstock genotype and environment influences, whereas bacterial communities of leaves and berries displayed associations with time.<br><br>CONCLUSIONS: These results provide further evidence of a microbial terroir within the grapevine root systems but also reveal that the microbiota of above-ground compartments are only weakly associated with the local soil microbiome in the Central Valley of California.}, }
@article {pmid37996810, year = {2023}, author = {Hülpüsch, C and Rauer, L and Nussbaumer, T and Schwierzeck, V and Bhattacharyya, M and Erhart, V and Traidl-Hoffmann, C and Reiger, M and Neumann, AU}, title = {Benchmarking MicrobIEM - a user-friendly tool for decontamination of microbiome sequencing data.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {269}, pmid = {37996810}, issn = {1741-7007}, abstract = {BACKGROUND: Microbiome analysis is becoming a standard component in many scientific studies, but also requires extensive quality control of the 16S rRNA gene sequencing data prior to analysis. In particular, when investigating low-biomass microbial environm