@article {pmid37263571, year = {2023}, author = {Im, ST and Mun, H and Park, S and Kang, H and Kim, WC and Heo, SJ and Lee, SH}, title = {Ishige okamurae Celluclast extract ameliorates non-alcoholic fatty liver in high-fructose diet-fed mice by modulation of lipid metabolism and gut microbiota composition.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {}, number = {}, pages = {113864}, doi = {10.1016/j.fct.2023.113864}, pmid = {37263571}, issn = {1873-6351}, abstract = {Recently, a new mechanism has revealed that gut microbiota plays a pivotal role in metabolizing fructose to acetate that facilitates hepatic lipogenesis. Therefore, our study investigated the role of microbiome on abnormal lipid synthesis in the presence of fructose and identified attenuating effects of Ishige okamurae Celluclast extract (IOCE) against fructose-induced fatty liver. The results indicated that oral administration of IOCE (150 and 300 mg/kg/day for 12 weeks) significantly reduced both gut microbiota-mediated and -non-mediated hepatic lipogenesis simultaneously triggered by fructose metabolism. IOCE reduced hepatic triglyceride accumulation and expression levels of key enzymes for glucolipid metabolism. In addition, IOCE regulated fatty acid synthesis, β-oxidation, and improved hepatic inflammation. Furthermore, IOCE inhibited direct fructose-to-acetate conversion and altered the compositions of gut microbiota. These findings suggest that IOCE might serve as a potential prebiotic dietary supplement by ameliorating fatty liver through dual regulation of classical lipogenic pathway and gut microbiota.}, }
@article {pmid37263544, year = {2023}, author = {Sumiyoshi, A and Fujii, H and Okuma, Y}, title = {Targeting microbiome, drug metabolism, and drug delivery in oncology.}, journal = {Advanced drug delivery reviews}, volume = {}, number = {}, pages = {114902}, doi = {10.1016/j.addr.2023.114902}, pmid = {37263544}, issn = {1872-8294}, abstract = {Recent emerging scientific evidence shows a relationship between gut microbiota (GM) and immunomodulation. In the recently published "Hallmarks of Cancer", the microbiome has been reported to play a crucial role in cancer research, and perspectives for its clinical implementation to improve the effectiveness of pharmacotherapy were explored. Several studies have shown that GM can affect the outcomes of pharmacotherapy in cancer, suggesting that GM may affect anti-tumor immunity. Thus, studies on GM that analyze big data using computer-based analytical methods are required. To deliver GM to an environment that favors the growth of immune cells inside and outside the tumor microenvironment (TME), several challenges need to be overcome for each delivery method (oral, endoscopic, and intravenous). Clinical trials are in progress to evaluate the effects of targeting GM and whether it can enhance immunity or act on the TME, thereby to improve the clinical outcomes for cancer patients.}, }
@article {pmid37263539, year = {2023}, author = {Rodrigues E-Lacerda, R and Fang, H and Robin, N and Bhatwa, A and Marko, DM and Schertzer, JD}, title = {Microbiota and Nod-like receptors balance inflammation and metabolism during obesity and diabetes.}, journal = {Biomedical journal}, volume = {}, number = {}, pages = {100610}, doi = {10.1016/j.bj.2023.100610}, pmid = {37263539}, issn = {2320-2890}, abstract = {Gut microbiota influence host immunity and metabolism during obesity. Bacterial sensors of the innate immune system relay signals from specific bacterial components (i.e., postbiotics) that can have opposing outcomes on host metabolic inflammation. NOD-like receptors (NLRs) such as Nod1 and Nod2 both recruit receptor-interacting protein kinase 2 (RIPK2) but have opposite effects on blood glucose control. Nod1 connects bacterial cell wall-derived signals to metabolic inflammation and insulin resistance, whereas Nod2 can promote immune tolerance, insulin sensitivity, and better blood glucose control during obesity. NLR family pyrin domain containing (NLRP) inflammasomes can also generate divergent metabolic outcomes. NLRP1 protects against obesity and metabolic inflammation potentially because of a bias toward IL-18 regulation, whereas NLRP3 appears to have a bias toward IL-1β-mediated metabolic inflammation and insulin resistance. Targeting specific postbiotics that improve immunometabolism is a key goal. The Nod2 ligand, muramyl dipeptide (MDP) is a short-acting insulin sensitizer during obesity or during inflammatory lipopolysaccharide (LPS) stress. LPS with underacylated lipid-A antagonizes TLR4 and counteracts the metabolic effects of inflammatory LPS. Providing underacylated LPS derived from Rhodobacter sphaeroides improved insulin sensitivity in obese mice. Therefore, certain types of LPS can generate metabolically beneficial metabolic endotoxemia. Engaging protective adaptive immunoglobulin immune responses can also improve blood glucose during obesity. A bacterial vaccine approach using an extract of the entire bacterial community in the upper gut promotes protective adaptive immune response and long-lasting improvements in blood glucose control. A key future goal is to identify and combine postbiotics that cooperate to improve blood glucose control.}, }
@article {pmid37263438, year = {2023}, author = {Phulpoto, AH and Pirzada, T and Kanhar, NA}, title = {Exploring community dynamics: Cultivable and uncultivable for the microbial-mediated bioremediation of oil-based paints polluted soil from aqueous media by Plackett-Burman statistically designed conditions.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164505}, doi = {10.1016/j.scitotenv.2023.164505}, pmid = {37263438}, issn = {1879-1026}, abstract = {Oil-based paint seriously threatens biodiversity due to its complex composition and biocide toxicity. Therefore, it alters the microbial diversity abundance and in modern approaches like metagenomic, a powerful tool to get insight into pollutants effect on soil microbial community abundance. Thus, present study aimed at "exploring community dynamics: cultivable and uncultivable for the microbial-mediated bioremediation of oil-based paints polluted soil from aqueous media by Plackett-Burman statistical designed conditions". The total DNA from oil-based paints polluted soil was extracted by PowerSoil DNA Isolation Kit. The 16S rDNA genes were amplified using universal primers and PCR amplicons were sequenced for analysis of metagenomes to determine the bacterial microbiome abundance. A total 133,140 sequence reads, 2857 Operational Taxonomic Units (OTUs) of 16S rRNA genes, and 30 bacterial phyla were retrieved from all the oil-based paints polluted samples (C, R498, B698 and G492) with the significant increase in Firmicutes (18.90 %, 52.39 %, 49.75 %, 44.36 %) and Actinobacteria (26.66 %, 28.93 %, 28.17 %, 14.68 %) whereas a decrease in Proteobacteria (19.53 %, 6.32 %, 9.37 %, 16.21 %), Chloroflexi (16.93 %, 8.71 %, 9.78 %, 18.17 %), and Bacteroidetes (8.96 %, 0.36 %, 0.41 %, 0.11 %) was recorded respectively. Additionally, the 100 % removal of oil-based paints (R498, B698 and G492) was achieved by the cultivable microbial consortia in laboratory settings. On the other hand for the R498 single cultivable pure isolates exhibited biodegradation potential as "PDB20, 91 %", "PDB14, 81 %", and "PDB16, 87 %" while for the blue B698, "PDB4, 86 %", "PDB20, 89 %", "PDB5, and PDB2, 80%". Moreover, in case of G492, maximum % removal was achieved with "PDB20, 93 %", "PDB5, 90 %", "PDB6, 90 %", "PDB16, 88 %", "PDB2, and PDB4, 89%". Conclusively, in comparison to R498 and B698, maximum percent removal was displayed by G492 and this might be attributed due to difference in pigment. Cultivable consortia and individual pure isolates demonstrated >80 % contribution in the % removal of oil-based paints.}, }
@article {pmid37263432, year = {2023}, author = {Wu, X and Bei, S and Zhou, X and Luo, Y and He, Z and Song, C and Yuan, H and Pivato, B and Liesack, W and Peng, J}, title = {Metagenomic insights into genetic factors driving bacterial niche differentiation between bulk and rhizosphere soils.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164221}, doi = {10.1016/j.scitotenv.2023.164221}, pmid = {37263432}, issn = {1879-1026}, abstract = {Cellular motility is crucial for effective colonization of the rhizosphere, but it is not yet clear whether bacterial motility is particularly linked to other genetic traits. Here, we applied genome-resolved metagenomics and phylogenomics to investigate the ecological significance of cellular motility for niche differentiation and the links between the genetic makeup of motile bacteria and rhizosphere colonization within a four-decade maize field experiment. Indeed, highly diverse sets of genes encoding cellular motility, including chemotaxis, flagellar assembly and motility proteins, and utilization of polymeric carbon were the important predictors of bacterial niche differentiation between bulk and rhizosphere soils. This is well exemplified by metagenome-assembled genomes encoding high motility capacity (hmc_MAGs). Their collective abundance was, on average, sixfold higher in rhizosphere soil than in bulk soil. All bulk-soil-derived MAGs showed low motility capacities (lmc). The hmc_MAGs were highly enriched in beneficial traits involved in carbohydrate utilization, assimilatory (nasA) and dissimilatory (nirBD) nitrate reduction, inorganic phosphate solubilization (gcd), and organic phosphate mineralization (phoD). Belonging to the families Sphingomonadaceae, Burkholderiaceae and Steroidobacteraceae, the hmc_MAGs showed a ninefold greater enrichment in these traits than proteobacterial lmc_MAGs and a twofold greater enrichment than 264 genomes publicly available for the above three families, thereby substantiating that a specific rhizosphere effect acted on the microbes represented by the hmc_MAGs. The particular link between the genetic capacities for high cellular motility and increased carbohydrate depolymerization as the key determinant for plant-selected rhizosphere colonization was further substantiated by the analysis of public bulk-rhizosphere soil metagenomes retrieved from wheat and cucumber field sites.}, }
@article {pmid37263307, year = {2023}, author = {Raygoza Garay, JA and Turpin, W and Lee, SH and Smith, MI and Goethel, A and Griffiths, AM and Moayyedi, P and Espin-Garcia, O and Abreu, M and Aumais, GL and Bernstein, CN and Biron, IA and Cino, M and Deslandres, C and Dotan, I and El-Matary, W and Feagan, B and Guttman, DS and Huynh, H and Dieleman, LA and Hyams, JS and Jacobson, K and Mack, D and Marshall, JK and Otley, A and Panaccione, R and Ropeleski, M and Silverberg, MS and Steinhart, AH and Turner, D and Yerushalmi, B and Paterson, AD and Xu, W and ,  and Croitoru, K}, title = {Gut Microbiome Composition is associated with future onset of Crohn's Disease in Healthy First-Degree Relatives.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2023.05.032}, pmid = {37263307}, issn = {1528-0012}, abstract = {BACKGROUND AND AIMS: The cause of Crohn's Disease (CD) is unknown, but the current hypothesis is that microbial or environmental factors induce gut inflammation in genetically susceptible individuals, leading to chronic intestinal inflammation. Case-control studies of CD patients have catalogued alterations in the gut microbiome composition; however, these studies fail to distinguish if the altered gut microbiome composition is associated with initiation of CD or is the result of inflammation or drug treatment.<br><br>METHODS: In this prospective cohort study, 3483 healthy first-degree relatives (FDRs) of patients with CD were recruited to identify the gut microbiome composition that precedes the onset of CD and to what extent this composition predicts the risk of developing CD. We applied a machine learning approach to the analysis of the gut microbiome composition (based on 16S rDNA sequencing) to define a microbial signature that associates with future development of CD. The performance of the model was assessed in an independent validation cohort.<br><br>RESULTS: In the validation cohort, the microbiome risk score (MRS) model yielded a hazard ratio (HR) of 2.24, 95% CI [1.03, 4.84], and a p-value =0.04, using the median of the MRS from the discovery cohort as the threshold. The MRS demonstrated a temporal validity by capturing individuals that developed CD up to five years prior to disease onset (AUC > 0.65). The five most important taxa contributing to the MRS included Ruminococcus torques, Blautia, Colidextribacter, an uncultured genus-level group from Oscillospiraceace, and Roseburia.<br><br>CONCLUSION: This study is the first to demonstrate that gut microbiome composition is associated with future onset of CD and suggests that gut microbiome is a contributor in the pathogenesis of CD.}, }
@article {pmid37263302, year = {2023}, author = {Kostenko, S and Khatua, B and Trivedi, S and Pillai, AN and McFayden, B and Morsy, M and Rajalingamgari, P and Sharma, V and Noel, P and Patel, K and El-Kurdi, B and Borges da Silva, H and Chen, X and Chandan, V and Navina, S and Vela, S and Cartin-Ceba, R and Snozek, C and Singh, VP}, title = {Amphipathic liponecrosis impairs bacterial clearance and causes infection during sterile inflammation.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2023.05.034}, pmid = {37263302}, issn = {1528-0012}, abstract = {BACKGROUND: While transient bacteremia is common during dental and endoscopic procedures, infections developing during sterile diseases like acute pancreatitis (AP) can have grave consequences. Here we examined how impaired bacterial clearance may cause this transition.<br><br>METHODS: Blood samples of AP patients, normal controls, and rodents with pancreatitis or those administered different non-esterified fatty acids (NEFA) were analyzed for albumin unbound NEFA, microbiome, and inflammatory cell injury. Macrophage uptake of unbound-NEFA using a novel coumarin tracer were done, and the downstream effects, NEFA-membrane phospholipid (phosphatidylcholine; PC) interactions were studied on isothermal titration calorimetry (ITC) RESULTS: Infected AP patients had higher circulating unsaturated NEFA, unbound-NEFA including linoleic acid (LA) and oleic acid (OA), higher bacterial 16S DNA, mitochondrial DNA, altered beta-diversity, enrichment in Pseudomonadales and increased annexin V positive myeloid (CD14) and CD3 positive T cells on admission. These, and increased circulating dead inflammatory cells were also noted in rodents with unbound unsaturated-NEFA. ITC showed progressively stronger unbound-LA interactions with aqueous media, PC, cardiolipin and albumin. Unbound-NEFA were taken into protein free membranes, cells, mitochondria, inducing voltage dependent anion channel oligomerization, reducing ATP, and impairing phagocytosis. These were reversed by albumin. In-vivo unbound-LA, OA increased bacterial loads and impaired phagocytosis, causing infection. LA, OA were more potent for these amphipathic interactions than the hydrophobic palmitic acid.<br><br>CONCLUSIONS: Release of stored LA, OA can increase their circulating unbound levels and cause amphipathic liponecrosis of immune cells via uptake by membrane phospholipids. This impairs bacterial clearance and causes infection during sterile inflammation.}, }
@article {pmid37262934, year = {2023}, author = {Fu, X and Hafza, N and Götz, F and Lämmerhofer, M}, title = {Profiling of branched chain and straight chain saturated fatty acids by ultra-high performance liquid chromatography-mass spectrometry.}, journal = {Journal of chromatography. A}, volume = {1703}, number = {}, pages = {464111}, doi = {10.1016/j.chroma.2023.464111}, pmid = {37262934}, issn = {1873-3778}, abstract = {Branched chain fatty acids (BCFAs) are one of the important sub categories of fatty acids (FAs) which have unique functions in nature. They are commonly analyzed by GC-MS after derivatization to methyl esters (FAMEs). On the other hand, there is a lack of isomer-selective LC-MS methods which allow the distinction of different isomers with wide coverage of carbon chain length. In this work, a systematic retention and isomer selectivity study on seven commercially available UHPLC columns (six polysaccharide columns Chiralpak IA-U, IB-U, IC-U, ID-U, IG-U and IH-U; one Acquity UPLC CSH C18 column) was performed. Various experimental factors were evaluated including column temperatures, gradient profiles and flow rates to elucidate their effects on the separation ability of homologous series of BCFAs with distinct chain lengths, different branching types and branching positions. In general, IG-U outperformed the other columns in terms of isomer selectivity especially for the short and medium-chain BCFA isomers while RP C18 showed good potential in terms of selectivity for long-chain BCFA isomers. Furthermore, after the evaluation of the chromatographic retention pattern on the various columns and method optimization, we report a methodology for untargeted isomer-selective BCFA profiling without precolumn derivatization with UHPLC-ESI-MS/MS by quadrupole-time-of-flight instrument with SWATH acquisition. The best method provides selectivity for constitutional isomers of BCFAs covering distinct chain length (C5-C20) with different branching types (methyl or ethyl) and branching positions (2Me, 3Me, 4Me, 6Me, anteiso and iso-BCFAs) with an optimized LC condition on Acquity UPLC CSH C18 column. Finally, the optimized method was applied for the BCFAs profiling in lipid extracts of Staphylococcus aureus samples. Besides, pooled human platelets and pooled human plasma were evaluated as mammalian samples for presence of BCFAs as well. The new method showed strong potential for BCFA profiling in bacterial samples including different isomers anteiso and iso-BCFAs, which could be a useful tool for related subdisciplines in metabolomics and lipidomics in particular in combination with electron-activated dissociation MS. Compared to GC, the presented isomer selective LC methods can be also of great utility for preparative purposes. Equivalent (carbon) chain length numbers were calculated for RP18 and Chiralpak IG-U and compared to those of FAMEs obtained by GC.}, }
@article {pmid37262358, year = {2023}, author = {Sharif, S and Oddie, SJ and Heath, PT and McGuire, W}, title = {Prebiotics to prevent necrotising enterocolitis in very preterm or very low birth weight infants.}, journal = {The Cochrane database of systematic reviews}, volume = {6}, number = {}, pages = {CD015133}, pmid = {37262358}, issn = {1469-493X}, abstract = {BACKGROUND: Dietary supplementation with prebiotic oligosaccharides to modulate the intestinal microbiome has been proposed as a strategy to reduce the risk of necrotising enterocolitis (NEC) and associated mortality and morbidity in very preterm or very low birth weight (VLBW) infants.<br><br>OBJECTIVES: To assess the benefits and harms of enteral supplementation with prebiotics (versus placebo or no treatment) for preventing NEC and associated morbidity and mortality in very preterm or VLBW infants.<br><br>SEARCH METHODS: We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, Embase, the Maternity and Infant Care database and the Cumulative Index to Nursing and Allied Health Literature (CINAHL), from the earliest records to July 2022. We searched clinical trials databases and conference proceedings, and examined the reference lists of retrieved articles.<br><br>SELECTION CRITERIA: We included randomised controlled trials (RCTs) and quasi-RCTs comparing prebiotics with placebo or no prebiotics in very preterm (< 32 weeks' gestation) or VLBW (< 1500 g) infants. The primary outcomes were NEC and all-cause mortality, and the secondary outcomes were late-onset invasive infection, duration of hospitalisation since birth, and neurodevelopmental impairment.<br><br>DATA COLLECTION AND ANALYSIS: Two review authors separately evaluated risk of bias of the trials, extracted data, and synthesised effect estimates using risk ratio (RR), risk difference (RD), and mean difference (MD), with associated 95% confidence intervals (CIs). The primary outcomes of interest were NEC and all-cause mortality; our secondary outcome measures were late-onset (> 48 hours after birth) invasive infection, duration of hospitalisation, and neurodevelopmental impairment. We used the GRADE approach to assess the level of certainty of the evidence.<br><br>MAIN RESULTS: We included seven trials in which a total of 705 infants participated. All the trials were small (mean sample size 100). Lack of clarity on methods to conceal allocation and mask caregivers or investigators were potential sources of bias in three of the trials. The studied prebiotics were fructo- and galacto-oligosaccharides, inulin, and lactulose, typically administered daily with enteral feeds during birth hospitalisation. Meta-analyses of data from seven trials (686 infants) suggest that prebiotics may result in little or no difference in NEC (RR 0.97, 95% CI 0.60 to 1.56; RD none fewer per 1000, 95% CI 50 fewer to 40 more; low-certainty evidence), all-cause mortality (RR 0.43, 95% CI 0.20 to 0.92; 40 per 1000 fewer, 95% CI 70 fewer to none fewer; low-certainty evidence), or late-onset invasive infection (RR 0.79, 95% CI 0.60 to 1.06; 50 per 1000 fewer, 95% CI 100 fewer to 10 more; low-certainty evidence) prior to hospital discharge. The certainty of this evidence is low because of concerns about the risk of bias in some trials and the imprecision of the effect size estimates. The data available from one trial provided only very low-certainty evidence about the effect of prebiotics on measures of neurodevelopmental impairment (Bayley Scales of Infant Development (BSID) Mental Development Index score < 85: RR 0.84, 95% CI 0.25 to 2.90; very low-certainty evidence; BSID Psychomotor Development Index score < 85: RR 0.24, 95% 0.03 to 2.00; very low-certainty evidence; cerebral palsy: RR 0.35, 95% CI 0.01 to 8.35; very low-certainty evidence).<br><br>AUTHORS' CONCLUSIONS: The available trial data provide low-certainty evidence about the effects of prebiotics on the risk of NEC, all-cause mortality before discharge, and invasive infection, and very low-certainty evidence about the effect on neurodevelopmental impairment for very preterm or VLBW infants. Our confidence in the effect estimates is limited; the true effects may be substantially different. Large, high-quality trials are needed to provide evidence of sufficient validity to inform policy and practice decisions.}, }
@article {pmid37261678, year = {2023}, author = {Ruggiero, AD and Vemuri, R and Blawas, M and Long, M and DeStephanis, D and Williams, AG and Chen, H and Justice, JN and Macauley, SL and Day, SM and Kavanagh, K}, title = {Long-term dasatinib plus quercetin effects on aging outcomes and inflammation in nonhuman primates: implications for senolytic clinical trial design.}, journal = {GeroScience}, volume = {}, number = {}, pages = {}, pmid = {37261678}, issn = {2509-2723}, abstract = {Cellular senescence increases with aging and results in secretion of pro-inflammatory factors that induce local and systemic tissue dysfunction. We conducted the first preclinical trial in a relevant middle-aged nonhuman primate (NHP) model to allow estimation of the main translatable effects of the senolytic combination dasatinib (D) and quercetin (Q), with and without caloric restriction (CR). A multi-systemic survey of age-related changes, including those on immune cells, adipose tissue, the microbiome, and biomarkers of systemic organ and metabolic health are reported. Age-, weight-, sex-, and glycemic control-matched NHPs (D + Q, n = 9; vehicle [VEH] n = 7) received two consecutive days of D + Q (5 mg/kg + 50 mg/kg) monthly for 6 months, where in month six, a 10% CR was implemented in both D + Q and VEH NHPs to induce equal weight reductions. D + Q reduced senescence marker gene expressions in adipose tissue and circulating PAI-1 and MMP-9. Improvements were observed in immune cell types with significant anti-inflammatory shifts and reductions in microbial translocation biomarkers, despite stable microbiomes. Blood urea nitrogen showed robust improvements with D + Q. CR resulted in significant positive body composition changes in both groups with further improvement in immune cell profiles and decreased GDF15 (p = 0.05), and the interaction of D + Q and CR dramatically reduced glycosylated hemoglobin A1c (p = 0.03). This work indicates that 6 months of intermittent D + Q exposure is safe and may combat inflammaging via immune benefits and improved intestinal barrier function. We also saw renal benefits, and with CR, improved metabolic health. These data are intended to provide direction for the design of larger controlled intervention trials in older patients.}, }
@article {pmid37261580, year = {2023}, author = {Li, Q and Yi, X and Li, L and Sun, Y and Nie, Z and Du, J and Cao, L and Gao, J and Xu, G}, title = {Effects of effective microorganisms on the physiological status, intestinal microbiome, and serum metabolites of Eriocheir sinensis.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {37261580}, issn = {1618-1905}, abstract = {The compound known as effective microorganisms (EMs) is widely used in aquaculture to improve water quality, but how they affect the health of Chinese mitten crab (Eriocheir sinensis) is unclear, especially in terms of intestinal microbiota and serum metabolites. In this study, we fed juvenile crabs with an EM-containing diet to explore the effects of EM on the physiological status, intestinal microbiome, and metabolites of E. sinensis. The activities of alanine aminotransferase and alkaline phosphatase were significantly enhanced by EM, indicating that EM supplementation effectively enhanced the antioxidant capacity of E. sinensis. Proteobacteria, Tenericutes, Firmicutes, Bacteroidetes, and Actinobacteria were the main intestinal microbes in both the control and EM groups. Linear discriminant effect size analysis showed that Fusobacteriaceae, Desulfovibrio, and Morganella were biomarkers in the control group, and Exiguobacterium and Rhodobacteraceae were biomarkers in the EM group. Metabolomics analysis revealed that EM supplementation increased cellular energy sources and decreased protein consumption, and oxidative stress. Together, these results indicate that EM can optimize the intestinal microbiome and serum metabolites, thereby benefiting the health of E. sinensis.}, }
@article {pmid37261548, year = {2023}, author = {Hong, H and Wang, L and Qi, Y}, title = {Characteristics of the oropharyngeal microbiota among infants with pneumonia and their effects on immune response and subsequent respiratory morbidity.}, journal = {European journal of pediatrics}, volume = {}, number = {}, pages = {}, pmid = {37261548}, issn = {1432-1076}, abstract = {UNLABELLED: Changes in airway microbiota among infants with pneumonia and their impact on subsequent respiratory health are largely unknown. The present study aimed to analyze the oropharyngeal microbiota of infants with pneumonia and to explore the impact of disturbances of the microbiota on disease severity and long-term respiratory morbidities. The oropharyngeal microbiome was characterized using 16S ribosomal RNA-based sequencing, while serum immune mediators were assessed using cytometric bead array, and invariant natural killer T (iNKT) cells were detected using flow cytometry in infants with pneumonia < 6 months of age. Patients were followed up to 3 years of age, and clinical and respiratory morbidity data were collected. A total of 106 infants with pneumonia were enrolled in this study. Diversity of the respiratory microbiota was inversely correlated with the severity of pneumonia and length of hospitalization. Patients who experienced wheezing during pneumonia exhibited lower percentages of total iNKT cells, CD8-positive (+), and CD4-CD8- subsets, and higher CD4 + subsets than those without. The relative abundances of Prevotella and Veillonella species were lower in patients with severe pneumonia. The abundance of Veillonella was higher in patients who experienced wheezing during pneumonia and in those with subsequent recurrent wheezing than in those without wheezing. The relative abundance and total counts of Bifidobacterium, Lactobacillus, and Neisseria were higher in patients who did not experience subsequent recurrent wheezing.<br><br>CONCLUSIONS: Diversity of the respiratory microbiota was inversely associated with pneumonia severity, and the percentage of iNKT cells was associated with wheezing during pneumonia. Several species may be associated with subsequent respiratory morbidities and warrant further investigation.<br><br>WHAT IS KNOWN: &#x2022;&#xa0;Early life airway microbiota symbiosis affects the severity of respiratory infection&#xa0;and the risk for the development of asthma. &#x2022;&#xa0;Changes in airway microbiota among infants with pneumonia and their impact on&#xa0;subsequent respiratory health are largely unknown.<br><br>WHAT IS NEW: &#x2022;&#xa0;The diversity of the airway microbiome was inversely associated with the severity&#xa0;of pneumonia and length of hospitalization. &#x2022;&#xa0;The abundance of Veillonella was higher in patients who experienced wheezing&#xa0;during pneumonia and in those with subsequent recurrent wheezing.}, }
@article {pmid37261348, year = {2023}, author = {Singh, A and Alexander, SG and Martin, S}, title = {Gut microbiome homeostasis and the future of probiotics in cancer immunotherapy.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1114499}, pmid = {37261348}, issn = {1664-3224}, abstract = {The gut microbiome has an impact on cancer immune surveillance and immunotherapy, with recent studies showing categorical differences between immunotherapy-sensitive and immunotherapy-resistant cancer patient cohorts. Although probiotics are traditionally being supplemented to promote treatments or sustain therapeutic benefits; the FDA has not approved any for use with immunotherapy. The first step in developing probiotics for immunotherapy is identifying helpful or harmful bacteria down to the strain level. The gut microbiome's heterogeneity before and during treatment is also being investigated to determine microbial strains that are important for immunotherapy. Moreover, Dietary fiber intake, prebiotic supplementation and fecal microbiota transplantation (FMT) were found to enhance intratumoral CD8+ T cell to T-reg ratio in the clinics. The possibility of probiotic immunotherapy as a "living adjuvant" to CAR treatment and checkpoint blockade resistance is actively being investigated.}, }
@article {pmid37260833, year = {2023}, author = {Myers, KS and Ingle, AT and Walters, KA and Fortney, NW and Scarborough, MJ and Donohue, TJ and Noguera, DR}, title = {Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {11}, number = {}, pages = {1197175}, pmid = {37260833}, issn = {2296-4185}, abstract = {The liquid residue resulting from various agroindustrial processes is both rich in organic material and an attractive source to produce a variety of chemicals. Using microbial communities to produce chemicals from these liquid residues is an active area of research, but it is unclear how to deploy microbial communities to produce specific products from the different agroindustrial residues. To address this, we fed anaerobic bioreactors one of several agroindustrial residues (carbohydrate-rich lignocellulosic fermentation conversion residue, xylose, dairy manure hydrolysate, ultra-filtered milk permeate, and thin stillage from a starch bioethanol plant) and inoculated them with a microbial community from an acid-phase digester operated at the wastewater treatment plant in Madison, WI, United States. The bioreactors were monitored over a period of months and sampled to assess microbial community composition and extracellular fermentation products. We obtained metagenome assembled genomes (MAGs) from the microbial communities in each bioreactor and performed comparative genomic analyses to identify common microorganisms, as well as any community members that were unique to each reactor. Collectively, we obtained a dataset of 217 non-redundant MAGs from these bioreactors. This metagenome assembled genome dataset was used to evaluate whether a specific microbial ecology model in which medium chain fatty acids (MCFAs) are simultaneously produced from intermediate products (e.g., lactic acid) and carbohydrates could be applicable to all fermentation systems, regardless of the feedstock. MAGs were classified using a multiclass classification machine learning algorithm into three groups, organisms fermenting the carbohydrates to intermediate products, organisms utilizing the intermediate products to produce MCFAs, and organisms producing MCFAs directly from carbohydrates. This analysis revealed common biological functions among the microbial communities in different bioreactors, and although different microorganisms were enriched depending on the agroindustrial residue tested, the results supported the conclusion that the microbial ecology model tested was appropriate to explain the MCFA production potential from all agricultural residues.}, }
@article {pmid37260751, year = {2023}, author = {Gaeta, AL and Willicott, K and Willicott, CW and McKay, LE and Keogh, CM and Altman, TJ and Kimble, LC and Yarbrough, AL and Caldwell, KA and Caldwell, GA}, title = {Mechanistic impacts of bacterial diet on dopaminergic neurodegeneration in a Caenorhabditis elegans α-synuclein model of Parkinson's disease.}, journal = {iScience}, volume = {26}, number = {6}, pages = {106859}, pmid = {37260751}, issn = {2589-0042}, abstract = {Failure of inherently protective cellular processes and misfolded protein-associated stress contribute to the progressive loss of dopamine (DA) neurons characteristic of Parkinson's disease (PD). A disease-modifying role for the microbiome has recently emerged in PD, representing an impetus to employ the soil-dwelling nematode, Caenorhabditis elegans, as a preclinical model to correlate changes in gene expression with neurodegeneration in transgenic animals grown on distinct bacterial food sources. Even under tightly controlled conditions, hundreds of differentially expressed genes and a robust neuroprotective response were discerned between clonal C. elegans strains overexpressing human alpha-synuclein in the DA neurons fed either one of only two subspecies of Escherichia coli. Moreover, this neuroprotection persisted in a transgenerational manner. Genetic analysis revealed a requirement for the double-stranded RNA (dsRNA)-mediated gene silencing machinery in conferring neuroprotection. In delineating the contribution of individual genes, evidence emerged for endopeptidase activity and heme-associated pathway(s) as mechanistic components for modulating dopaminergic neuroprotection.}, }
@article {pmid37260707, year = {2023}, author = {Li, X and Yi, Y and Wu, T and Chen, N and Gu, X and Xiang, L and Jiang, Z and Li, J and Jin, H}, title = {Integrated microbiome and metabolome analysis reveals the interaction between intestinal flora and serum metabolites as potential biomarkers in hepatocellular carcinoma patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1170748}, pmid = {37260707}, issn = {2235-2988}, abstract = {Globally, liver cancer poses a serious threat to human health and quality of life. Despite numerous studies on the microbial composition of the gut in hepatocellular carcinoma (HCC), little is known about the interactions of the gut microbiota and metabolites and their role in HCC. This study examined the composition of the gut microbiota and serum metabolic profiles in 68 patients with HCC, 33 patients with liver cirrhosis (LC), and 34 healthy individuals (NC) using a combination of metagenome sequencing and liquid chromatography-mass spectrometry (LC-MS). The composition of the serum metabolites and the structure of the intestinal microbiota were found to be significantly altered in HCC patients compared to non-HCC patients. LEfSe and metabolic pathway enrichment analysis were used to identify two key species (Odoribacter splanchnicus and Ruminococcus bicirculans) and five key metabolites (ouabain, taurochenodeoxycholic acid, glycochenodeoxycholate, theophylline, and xanthine) associated with HCC, which then were combined to create panels for HCC diagnosis. The study discovered that the diagnostic performance of the metabolome was superior to that of the microbiome, and a panel comprised of key species and key metabolites outperformed alpha-fetoprotein (AFP) in terms of diagnostic value. Spearman's rank correlation test was used to determine the relationship between the intestinal flora and serum metabolites and their impact on hepatocarcinogenesis and progression. A random forest model was used to assess the diagnostic performance of the different histologies alone and in combination. In summary, this study describes the characteristics of HCC patients' intestinal flora and serum metabolism, demonstrates that HCC is caused by the interaction of intestinal flora and serum metabolites, and suggests that two key species and five key metabolites may be potential markers for the diagnosis of HCC.}, }
@article {pmid37260691, year = {2023}, author = {Dlamini, P and Sekhohola-Dlamini, LM and Cowan, AK}, title = {Editorial: Soil-microbial interactions.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1213834}, pmid = {37260691}, issn = {1664-302X}, }
@article {pmid37260685, year = {2023}, author = {Amato, P and Mathonat, F and Nuñez Lopez, L and Péguilhan, R and Bourhane, Z and Rossi, F and Vyskocil, J and Joly, M and Ervens, B}, title = {The aeromicrobiome: the selective and dynamic outer-layer of the Earth's microbiome.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1186847}, pmid = {37260685}, issn = {1664-302X}, abstract = {The atmosphere is an integral component of the Earth's microbiome. Abundance, viability, and diversity of microorganisms circulating in the air are determined by various factors including environmental physical variables and intrinsic and biological properties of microbes, all ranging over large scales. The aeromicrobiome is thus poorly understood and difficult to predict due to the high heterogeneity of the airborne microorganisms and their properties, spatially and temporally. The atmosphere acts as a highly selective dispersion means on large scales for microbial cells, exposing them to a multitude of physical and chemical atmospheric processes. We provide here a brief critical review of the current knowledge and propose future research directions aiming at improving our comprehension of the atmosphere as a biome.}, }
@article {pmid37260683, year = {2023}, author = {Ashy, RA and Jalal, RS and Sonbol, HS and Alqahtani, MD and Sefrji, FO and Alshareef, SA and Alshehrei, FM and Abuauf, HW and Baz, L and Tashkandi, MA and Hakeem, IJ and Refai, MY and Abulfaraj, AA}, title = {Functional annotation of rhizospheric phageome of the wild plant species Moringa oleifera.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1166148}, pmid = {37260683}, issn = {1664-302X}, abstract = {INTRODUCTION: The study aims to describe phageome of soil rhizosphere of M.oleifera in terms of the genes encoding CAZymes and other KEGG enzymes.<br><br>METHODS: Genes of the rhizospheric virome of the wild plant species Moringa oleifera were investigated for their ability to encode useful CAZymes and other KEGG (Kyoto Encyclopedia of Genes and Genomes) enzymes and to resist antibiotic resistance genes (ARGs) in the soil.<br><br>RESULTS: Abundance of these genes was higher in the rhizospheric microbiome than in the bulk soil. Detected viral families include the plant viral family Potyviridae as well as the tailed bacteriophages of class Caudoviricetes that are mainly associated with bacterial genera Pseudomonas, Streptomyces and Mycobacterium. Viral CAZymes in this soil mainly belong to glycoside hydrolase (GH) families GH43 and GH23. Some of these CAZymes participate in a KEGG pathway with actions included debranching and degradation of hemicellulose. Other actions include biosynthesizing biopolymer of the bacterial cell wall and the layered cell wall structure of peptidoglycan. Other CAZymes promote plant physiological activities such as cell-cell recognition, embryogenesis and programmed cell death (PCD). Enzymes of other pathways help reduce the level of soil H2O2 and participate in the biosynthesis of glycine, malate, isoprenoids, as well as isoprene that protects plant from heat stress. Other enzymes act in promoting both the permeability of bacterial peroxisome membrane and carbon fixation in plants. Some enzymes participate in a balanced supply of dNTPs, successful DNA replication and mismatch repair during bacterial cell division. They also catalyze the release of signal peptides from bacterial membrane prolipoproteins. Phages with the most highly abundant antibiotic resistance genes (ARGs) transduce species of bacterial genera Pseudomonas, Streptomyces, and Mycobacterium. Abundant mechanisms of antibiotic resistance in the rhizosphere include "antibiotic efflux pump" for ARGs soxR, OleC, and MuxB, "antibiotic target alteration" for parY mutant, and "antibiotic inactivation" for arr-1.<br><br>DISCUSSION: These ARGs can act synergistically to inhibit several antibiotics including tetracycline, penam, cephalosporin, rifamycins, aminocoumarin, and oleandomycin. The study highlighted the issue of horizontal transfer of ARGs to clinical isolates and human gut microbiome.}, }
@article {pmid37260590, year = {2023}, author = {Ishimwe, JA and Kirabo, A}, title = {Editorial: Gut microbiome and metabolic physiology.}, journal = {Frontiers in physiology}, volume = {14}, number = {}, pages = {1216411}, pmid = {37260590}, issn = {1664-042X}, }
@article {pmid37260523, year = {2023}, author = {Yang, Y and Liu, J and Ou, H and Ma, X and Li, J and Shao, B and Jin, R and Zhao, J}, title = {Study on the Mechanism of Jiaotai Pill Intervention on Insomnia Animal Model Based on Gut Microbiome and Metabolomics.}, journal = {Evidence-based complementary and alternative medicine : eCAM}, volume = {2023}, number = {}, pages = {2442505}, pmid = {37260523}, issn = {1741-427X}, abstract = {BACKGROUND: With the continuous advancement of clinical application and experimental research of JTP, the application prospect of JTP in nervous system diseases and metabolic diseases is becoming increasingly clear. Jiaotai Pill (JTP) is a traditional Chinese medicine formula for insomnia, consisting of Coptidis rhizoma and Cinnamomi cortex, which dates back to Han Shi Yi Tong in the Ming Dynasty of China.<br><br>OBJECTIVE: Based on the brain-gut axis theory, this paper aims to explore the potential mechanism of JTP in the intervention of insomnia by using intestinal microbiome and metabolomics technology, taking the animal model of insomnia as the research object, so as to provide experimental basis for its further application and research.<br><br>METHODS: The insomnia mouse model was induced by intraperitoneal injection of para-chlorophenylalanine (PCPA). The clinical equivalent dose of JTP was administered by gavage for one week. The efficacy of JTP was evaluated by behavioral tests, serum biochemical detection, and brain histomorphological observation. The contents of cecum were analyzed by microbiomics and metabolomics.<br><br>RESULTS: The results show that insomnia caused by PCPA led to daytime dysfunction, higher HPA axis hormone levels, and morphologically impaired hippocampus. JTP reversed these anomalies. Omics research indicates that JTP significantly reduced gut &#x3b1; diversity; at the phylum level, JTP reduced the relative abundance of Firmicutes, Deferribacterota, Cyanobacteria, and Actinobacteriota and increased the relative abundance of Verrucomicrobiota, Proteobacteria, and Desulfobacterota. At the genus level, JTP reduced the relative abundance of Muribaculaceae, Lachnospiraceae_NK4A136_group, Alistipes, Colidextribacter, Muribaculum, and Mucispirillum and increased the relative abundance of Bacteroides and Akkermansia. JTP also reversed the activation of the linoleic acid metabolism pathway induced by insomnia. The combined analysis of omics suggests that JTP may play a role by regulating the inflammatory state of the body. Further gene expression analysis of brain tissue confirmed this.<br><br>CONCLUSIONS: We hypothesize that JTP may achieve insomnia relief by eliminating inflammation-causing bacteria in the gut and reducing inflammation levels through the brain-gut axis, pointing to potential targets and pathways for future research on JTP.}, }
@article {pmid37260512, year = {2023}, author = {Oulas, A and Minadakis, G and Zachariou, M and Tomazou, M and Vlamis-Gardikas, A and Spyrou, GM}, title = {Bacterial Wars-a tool for the prediction of bacterial predominance based on network analysis measures.}, journal = {NAR genomics and bioinformatics}, volume = {5}, number = {2}, pages = {lqad049}, pmid = {37260512}, issn = {2631-9268}, abstract = {Bacterial Wars (BW) is a network-based tool that applies a two-step pipeline to display information on the competition of bacterial species found in the same microbiome. It utilizes antimicrobial peptide (AMP) sequence similarities to obtain a relationship between species. The working hypothesis (putative AMP defense) is that friendly species share sequence similarity among the putative AMPs of their proteomes and are therefore immune to their AMPs. This may not happen in competing bacterial species with dissimilar putative AMPs. Similarities in the putative AMPs of bacterial proteomes may be thus used to predict predominance. The tool provides insights as to which bacterial species are more likely to 'die' in a competing environmental niche.}, }
@article {pmid37260411, year = {2023}, author = {Yue, K and Sheng, D and Xue, X and Zhao, L and Zhao, G and Jin, C and Zhang, L}, title = {Bidirectional Mediation Effects between Intratumoral Microbiome and Host DNA Methylation Changes Contribute to Stomach Adenocarcinoma.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0090423}, doi = {10.1128/spectrum.00904-23}, pmid = {37260411}, issn = {2165-0497}, abstract = {The induction of aberrant DNA methylation is the major pathway by which Helicobacter pylori infection induces stomach adenocarcinoma (STAD). The involvement of the non-H. pylori gastric microbiota in this mechanism remains to be examined. RNA sequencing data, clinical information, and DNA methylation data were obtained from The Cancer Genome Atlas (TCGA) STAD project. The Kraken 2 pipeline was employed to explore the microbiome profiles. The microbiome was associated with occurrence, distal metastasis, and prognosis, and differential methylation changes related to distal metastasis and prognosis were analyzed. Bi-directional mediation effects of the intratumoral microbiome and host DNA methylation changes on the metastasis and prognosis of STAD were identified by mediation analysis. The expression of the ZNF215 gene was verified by real-time quantitative PCR (RT-qPCR). A cell counting kit 8 (CCK8) cell proliferation experiment and a cell clone formation experiment were used to evaluate the proliferation and invasion abilities of gastric cells. Our analysis revealed that H. pylori and other cancer-related microorganisms were related to the occurrence, progression, or prognosis of STAD. The related methylated genes were particularly enriched in related cancer pathways. Kytococcus sedentarius and Actinomyces oris, which interacted strongly with methylation changes in immune genes, were associated with prognosis. Cell experiments verified that Staphylococcus saccharolyticus could promote the proliferation and cloning of gastric cells by regulating the gene expression level of the ZNF215 gene. Our study suggested that the bi-directional mediation effect between intratumoral microorganisms and host epigenetics was key to the distal metastasis of cancer cells and survival deterioration in the tumor microenvironment of stomach tissues of patients with STAD. IMPORTANCE The burgeoning field of oncobiome research declared that members of the intratumoral microbiome besides Helicobacter pylori existed in tumor tissues and participated in the occurrence and development of gastric cancer, and the methylation of host DNA may be a potential target of microbes and their metabolites. Current research focuses mostly on species composition, but the functional genes of the members of the microbiota are also key to their interaction with the host. Therefore, we focused on characterizing the species composition and functional gene composition of microbes in gastric cancer, and we suggest that microbes may further participate in the occurrence and development of cancer by influencing abnormal epigenetic changes in the host. Some key bioinformatics analysis results were verified by in vitro experiments. Thus, we consider that the tumor microbiota-host epigenetic axis of gastric cancer microorganisms and the host explains the mechanism of the microbiota participating in cancer occurrence and development, and we make some verifiable experimental predictions.}, }
@article {pmid37260391, year = {2023}, author = {Olofintila, OE and Noel, ZA}, title = {Soybean and Cotton Spermosphere Soil Microbiome Shows Dominance of Soilborne Copiotrophs.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0037723}, doi = {10.1128/spectrum.00377-23}, pmid = {37260391}, issn = {2165-0497}, abstract = {The spermosphere is the transient, immediate zone of soil around imbibing and germinating seeds. It represents a habitat where there is contact between seed-associated microbes and soil microbes, but it is studied less than other plant habitats. Previous studies on spermosphere microbiology were primarily culture based or did not sample the spermosphere soil as initially defined in space and time. Thus, the objectives of this study were to develop an efficient strategy to collect spermosphere soils around imbibing soybean and cotton in nonsterile soil and investigate changes in microbial communities. The method employed sufficiently collected spermosphere soil as initially defined in space by constraining the soil sampled with a cork borer and confining the soil to a 12-well microtiter plate. Spermosphere prokaryote composition changed over time and depended on the crop within 6 h after seeds were sown. By 12 to 18 h, crops had unique microbial communities in spermosphere soils. Prokaryote evenness dropped following seed imbibition, with the proliferation of copiotrophic soil bacteria. Due to their long history of plant growth promotion, prokaryote operational taxonomic units (OTUs) in Bacillus, Paenibacillus, Burkholderia, Massilia, Azospirillum, and Pseudomonas were notable organisms enriched. Fungi and prokaryotes were hub taxa in cotton and soybean spermosphere networks. Additionally, the enriched taxa were not hubs in networks, suggesting that other taxa besides those enriched may be important for spermosphere communities. Overall, this study advances knowledge in the assembly of the plant microbiome early in a plant's life, which may have plant health implications in more mature plant growth stages. IMPORTANCE The central hypothesis of this research was that plant species and seed exudate release would alter the assembly of microbes in the spermosphere soil. Our research investigated the response of microbes to the initial burst of nutrients into the spermosphere soil, filling knowledge gaps from previous studies that pregerminated seeds under sterile conditions. We identified several copiotrophic bacterial lineages with a long history of plant growth promotion proliferating in response to the initial exudate release. With a comparative network approach, we show that these copiotrophic bacteria are not central to networks, demonstrating that other microbes (including fungi) may be important for community structure. This study improves knowledge on microbial dynamics in the understudied spermosphere and helps inform solutions for biologically or ecologically motivated solutions to spermosphere pathogens.}, }
@article {pmid37260140, year = {2023}, author = {Zhang, H and Jin, K and Xiong, K and Jing, W and Pang, Z and Feng, M and Cheng, X}, title = {Disease-associated gut microbiome and critical metabolomic alterations in patients with colorectal cancer.}, journal = {Cancer medicine}, volume = {}, number = {}, pages = {}, doi = {10.1002/cam4.6194}, pmid = {37260140}, issn = {2045-7634}, abstract = {BACKGROUND: Gut microbiota plays a significant role in the colorectal cancer (CRC) process. Ectopic colonization of multiple oral bacteria is reportedly associated with CRC pathogenesis and progression, but the details remain unclear.<br><br>METHODS: We enrolled a cohort of 50 CRC patients and 52 healthy controls from an East China population. Taxonomic and functional analysis of the fecal microbiota were performed using 16S rDNA (50&#x2009;+&#x2009;52 samples) and shotgun metagenomic sequencing (8&#x2009;+&#x2009;6 samples), respectively, with particular attention paid to gut-colonized oral bacteria.<br><br>RESULTS AND CONCLUSIONS: The results showed more detected bacterial species but lower species evenness within the samples from CRC patients. To determine the specific bacteria enriched in each group, we analyzed their possible protective, carcinogenic, or opportunistic roles in the CRC process. Among the ectopic oral bacteria, we observed a significant increase in the abundance of Fusobacterium and decreased abundance of Prevotella and Ruminococcus in the CRC group. Main differences in the functional composition of these two groups were related to energy metabolism and biosynthesis, especially the glycolytic pathway. Furthermore, we validated the colonization of Fusobacterium nucleatum subsp. animalis within CRC tissues and studied its impact on the host intestinal epithelium and tumor cells. With high selectivity for cancerous tissues, this subspecies promoted CRC cell proliferation and induced potential DNA damage.}, }
@article {pmid37260059, year = {2023}, author = {Ammer-Herrmenau, C and Lingens, CHM and Ratei, CS and Heuer, C and Antweiler, K and Hamm, J and Buchholz, SM and Azizian, A and Ghadimi, M and Ellenrieder, V and Neesse, A}, title = {Whole 16S rRNA sequencing of the oral microbiome predicts postoperative pancreatic fistula: prospective observational cohort study.}, journal = {The British journal of surgery}, volume = {}, number = {}, pages = {}, doi = {10.1093/bjs/znad129}, pmid = {37260059}, issn = {1365-2168}, }
@article {pmid37260034, year = {2023}, author = {Kim, YH and Park, MR and Kim, SY and Kim, MY and Kim, KW and Sohn, MH}, title = {Respiratory microbiome profiles are associated with distinct inflammatory phenotype and lung function in children with asthma.}, journal = {Journal of investigational allergology &amp; clinical immunology}, volume = {}, number = {}, pages = {0}, doi = {10.18176/jiaci.0918}, pmid = {37260034}, issn = {1018-9068}, abstract = {BACKGROUND: Respiratory microbiome studies have fostered our understanding of various phenotypes and endotypes of heterogeneous asthma. However, the relationship between the respiratory microbiome and clinical phenotypes in children with asthma remains unclear. We aimed to identify microbiome-driven clusters reflecting the clinical features of asthma and their dominant microbiotas in children with asthma.<br><br>METHODS: Induced sputum was collected from children with asthma, and microbiome profiles were generated via sequencing of the V3-V4 region of the 16S rRNA gene. Cluster analysis was performed using the partitioning around medoid clustering method. The dominant microbiota in each cluster was determined using the Linear Discriminant Effect Size analysis. Each cluster was analyzed for association among the dominant microbiota, clinical phenotype, and inflammatory cytokine.<br><br>RESULTS: Eighty-three children diagnosed with asthma were evaluated. Among four clusters reflecting the clinical characteristics of asthma, cluster 1, dominated by Haemophilus and Neisseria, demonstrated lower post-bronchodilator (BD) forced expiratory volume in 1 second (FEV1)/forced vital capacity (FVC) than that in the other clusters and more mixed granulocytic asthma. Neisseria negatively correlated with pre-BD and post-BD FEV1/FVC. Haemophilus and Neisseria positively correlated with programmed death-ligand (PD-L)1.<br><br>CONCLUSION: To our knowledge, this study is the first to analyze the relationship between an unbiased microbiome-driven cluster and clinical phenotype in children with asthma. The cluster dominated by Haemophilus and Neisseria showed fixed airflow obstruction and mixed granulocytic asthma, which correlated with PD-L1 levels. Thus, microbiome-driven unbiased clustering can help identify new asthma phenotypes related to endotypes in childhood asthma.}, }
@article {pmid37259168, year = {2023}, author = {Wanelik, KM and Raulo, A and Troitsky, T and Husby, A and Knowles, SCL}, title = {Maternal transmission gives way to social transmission during gut microbiota assembly in wild mice.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {29}, pmid = {37259168}, issn = {2524-4671}, abstract = {BACKGROUND: The mammalian gut microbiota influences a wide array of phenotypes which are relevant to fitness, yet knowledge about the transmission routes by which gut microbes colonise hosts in natural populations remains limited. Here, we use an intensively studied wild population of wood mice (Apodemus sylvaticus) to examine how vertical (maternal) and horizontal (social) transmission routes influence gut microbiota composition throughout life.<br><br>RESULTS: We identify independent signals of maternal transmission (sharing of taxa between a mother and her offspring) and social transmission (sharing of taxa predicted by the social network), whose relative magnitudes shift as hosts age. In early life, gut microbiota composition is predicted by both maternal and social relationships, but by adulthood the impact of maternal transmission becomes undetectable, leaving only a signal of social transmission. By exploring which taxa drive the maternal transmission signal, we identify a candidate maternally-transmitted bacterial family in wood mice, the Muribaculaceae.<br><br>CONCLUSION: Overall, our findings point to an ontogenetically shifting transmission landscape in wild mice, with a mother's influence on microbiota composition waning as offspring age, while the relative impact of social contacts grows.}, }
@article {pmid37259058, year = {2023}, author = {Ma, L and Jiang, H and Han, T and Shi, Y and Wang, M and Jiang, S and Yang, S and Yao, L and Jia, Q and Shao, L}, title = {The menstrual cycle regularity and skin: irregular menstrual cycle affects skin physiological properties and skin bacterial microbiome in urban Chinese women.}, journal = {BMC women's health}, volume = {23}, number = {1}, pages = {292}, pmid = {37259058}, issn = {1472-6874}, abstract = {BACKGROUND: The regularity of the menstrual cycle directly affects women's health. Many studies have focused on menstrual health; however, menstrual cycle regularity-related variations in skin physiological characteristics and skin microbiota have been seldom investigated.<br><br>METHODS: To investigate the menstrual cycle regularity-related variations in skin physiological characteristics and skin microbiota of 197 cases of Chinese women aged 18-35&#xa0;years living in shanghai in 2021. Based on a self-evaluation questionnaire, the volunteers were divided into three groups C1 (those with a regular menstrual cycle), C2 (those with a less regular menstrual cycle) and C3 (those with an irregular menstrual cycle). The physiological parameters of facial skin were measured by non-invasive methods and the skin microbiome was analyzed by 16S rRNA high-throughput sequencing.<br><br>RESULTS: In the C3 group, the hydration content was significantly decreased (p&#x2009;<&#x2009;0.05), the TEWL was significantly increased (p&#x2009;<&#x2009;0.05), and the sebum content was increased (p&#x2009;>&#x2009;0.05), indicating that the skin barrier integrity weakened with increased menstrual cycle irregularity. Additionally, the melanin level, L value and b value were significantly decreased (p&#x2009;<&#x2009;0.05) in the C3 group, but the a value was significantly increased (p&#x2009;<&#x2009;0.001), which indicated that the skin color became darker. Furthermore, the skin microbiota diversity decreased with increasing cycle irregularity, but the differences were not significant. The skin microbiota composition showed that the proportion of Firmicutes, Acinetobacter, Staphylococcus and Cutibacterium were increased in those with an irregular menstrual cycle, indicating that alterations in the ratio of bacterial phyla and/or genera might disturb skin homeostasis. Spearman correlation analysis revealed strong correlations between the microbiota and skin physiological parameters. Based on the associations among hormones, skin physiological parameters and skin microbiota, it is possible that the skin physiological parameters, as well as the skin microbial diversity and composition, change with hormonal fluctuations during the menstrual cycle.<br><br>CONCLUSIONS: An irregular menstrual cycle can affect skin physiological characteristics and the skin microbiota. Female with an irregular menstrual cycle should strengthen skin care practices and use skin care products with moisturising and soothing effects to protect their skin.}, }
@article {pmid37258963, year = {2023}, author = {Hechard, T and Wang, H}, title = {Determination of Growth Rate and Virulence Plasmid Copy Number During Yersinia pseudotuberculosis Infection Using Droplet Digital PCR.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2674}, number = {}, pages = {101-115}, pmid = {37258963}, issn = {1940-6029}, abstract = {Pathogenic bacteria have evolved the ability to evade their host defenses and cause diseases. Virulence factors encompass a wide range of adaptations that allow pathogens to survive and proliferate in the hostile host environment during successful infection. In human pathogenic Yersinia species, the potent type III secretion system (T3SS) and other essential virulence factors are encoded on a virulence plasmid. Here, we investigated the bacterial growth rate and plasmid copy number following a Yersinia infection using droplet digital PCR (ddPCR). ddPCR is an exceptionally sensitive, highly precise, and cost-efficient method. It enables precise quantification even from very small amounts of target DNA. This method also enables analysis of complex samples with large amounts of interfering DNA, such as infected tissues or microbiome studies.}, }
@article {pmid37258874, year = {2023}, author = {Boctor, J and Oweda, M and El-Hadidi, M}, title = {Comprehensive Guideline for Microbiome Analysis Using R.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {393-436}, pmid = {37258874}, issn = {1940-6029}, abstract = {The need for a comprehensive consolidated guide for R packages and tools that are used in microbiome data analysis is significant; thus, we aim to provide a detailed step-by-step dissection of the most used R packages and tools in the field of microbiome data integration and analysis. The guideline aims to be a user-friendly simplification and tutorial on five main packages, namely phyloseq, MegaR, DADA2, Metacoder, and microbiomeExplorer due to their high efficiency and benefit in microbiome data analysis.}, }
@article {pmid37258868, year = {2023}, author = {Cheng, X and Joe, B}, title = {Artificial Intelligence in Medicine: Microbiome-Based Machine Learning for Phenotypic Classification.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {281-288}, pmid = {37258868}, issn = {1940-6029}, abstract = {Advanced computational approaches in artificial intelligence, such as machine learning, have been increasingly applied in life sciences and healthcare to analyze large-scale complex biological data, such as microbiome data. In this chapter, we describe the experimental procedures for using microbiome-based machine learning models for phenotypic classification.}, }
@article {pmid37258866, year = {2023}, author = {Arumugam, K and Bessarab, I and Haryono, MAS and Williams, RBH}, title = {Recovery and Analysis of Long-Read Metagenome-Assembled Genomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {235-259}, pmid = {37258866}, issn = {1940-6029}, abstract = {The development of long-read nucleic acid sequencing is beginning to make very substantive impact on the conduct of metagenome analysis, particularly in relation to the problem of recovering the genomes of member species of complex microbial communities. Here we outline bioinformatics workflows for the recovery and characterization of complete genomes from long-read metagenome data and some complementary procedures for comparison of cognate draft genomes and gene quality obtained from short-read sequencing and long-read sequencing.}, }
@article {pmid37258865, year = {2023}, author = {Bağcı, C and Albrecht, B and Huson, DH}, title = {MAIRA: Protein-based Analysis of MinION Reads on a Laptop.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {223-234}, pmid = {37258865}, issn = {1940-6029}, abstract = {Third-generation sequencing technologies are being increasingly used in microbiome research and this has given rise to new challenges in computational microbiome analysis. Oxford Nanopore's MinION is a portable sequencer that streams data that can be basecalled on-the-fly. Here we give an introduction to the MAIRA software, which is designed to analyze MinION sequencing reads from a microbiome sample, as they are produced in real-time, on a laptop. The software processes reads in batches and updates the presented analysis after each batch. There are two analysis steps: First, protein alignments are calculated to determine which genera might be present in a sample. When strong evidence for a genus is found, then, in a second step, a more detailed analysis is performed by aligning the reads against the proteins of all species in the detected genus. The program presents a detailed analysis of species, antibiotic resistance genes, and virulence factors.}, }
@article {pmid37258863, year = {2023}, author = {Jadeja, NB and Kapley, A}, title = {Designing Knowledge-Based Bioremediation Strategies Using Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {195-208}, pmid = {37258863}, issn = {1940-6029}, abstract = {Functional capacities for bioremediation are governed by metabolic mechanisms of inhabiting microbial communities at polluted niches. Process fluctuations lead to stress scenarios where microbes evolve continuously to adapt to sustain the harsh conditions. The biological wastewater treatment (WWT) process harbors the potential of these catabolic microbes for the degradation of organic molecules. In a typical biological WWT or soil bioremediation process, several microbial species coexist which code for enzymes that degrade complex compounds.High throughput DNA sequencing techniques for microbiome analysis in bioremediation processes have led to a powerful paradigm revealing the significance of metabolic functions and microbial diversity. The present chapter describes techniques in taxonomy and functional gene analysis for understanding bioremediation potential and novel strategies built on in silico analysis for the improvisation of existing aerobic wastewater treatment methods. Methods explaining comparative metagenomics by Metagenome Analysis server (MG-RAST) are described with successful case studies by focusing on industrial wastewaters and soil bioremediation studies.}, }
@article {pmid37258862, year = {2023}, author = {Arumugam, R and Ravichandran, P and Yeap, SK and Sharma, RSK and Zulkifly, SB and Yawah, D and Annavi, G}, title = {Application of High-Throughput Sequencing (HTS) to Enhance the Well-Being of an Endangered Species (Malayan Tapir): Characterization of Gut Microbiome Using MG-RAST.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {175-194}, pmid = {37258862}, issn = {1940-6029}, abstract = {The Tapirus indicus, also known as Malayan tapir, has been listed as a rapidly declining animal species in the past decades, along with being declared and categorized as an endangered species by the International Union for Conservation of Nature (IUCN) 2016. This tapir species is geographically distributed across several countries in Southeast Asia such as Peninsular Malaysia, Indonesia (Sumatra), South Thailand, and Myanmar. Amongst these countries, the Peninsula Malaysia forest is recorded to contain the highest number of Malayan tapir population. Unfortunately, in the past decades, the population of Malayan tapirs has declined swiftly due to serious deforestation, habitat fragmentation, and heavy vehicle accidents during road crossings at forest routes. Concerned by this predicament, the Department of Wildlife and National Parks (DWNP) Peninsular Malaysia collaborated with a few local universities to conduct various studies aimed at increasing the population number of tapirs in Malaysia. Several studies were conducted with the aim of enhancing the well-being of tapirs in captivity. Veterinarians face problems when it comes to selecting healthy and suitable tapirs for breeding programs at conservation centers. Conventional molecular methods using high-throughput sequencing provides a solution in determining the health condition of Malayan tapirs using the Next-Generation Sequencing (NGS) technology. Unaware by most, gut microbiome plays an important role in determining the health condition of an organism by various aspects: (1) digestion control; (2) benefiting the immune system; and (3) playing a role as a "second brain." Commensal gut bacterial communities (microbiomes) are predicted to influence organism health and disease. Imbalance of unhealthy and healthy microbes in the gut may contribute to weight gain, high blood sugar, high cholesterol, and other disorders. In infancy, neonatal gut microbiomes are colonized with maternal and environmental flora, and mature toward a stable composition in two to three years. Interactions between the microorganism communities and the host allow for the establishment of microbiological roles. Identifying the core microbiome(s) are essential in the prediction of diseases and changes in environmental behavior of microorganisms. The dataset of 16S rRNA amplicon sequencing of Malayan tapir was deposited in the MG-RAST portal. Parameters such as quality control, taxonomic prediction (unknown and predicted), diversity (rarefaction), and diversity (alpha) were analyzed using sequencing approaches (Amplicon sequencing). Comparisons of parameters, according to the type of sequencing, showed significant differences, except for the prediction variable. In the Amplicon sequencing datasets, the parameters Rarefaction and Unknown had the highest correlation, while Alpha and Predicted had the lowest. Firmicutes, Bacteroidetes, Proteobacteria, Bacilli, and Bacteroidia were the most representative genera in Malayan tapir amplicon sequences, which indicated that most of the tapirs were healthy. However, continuous assessment to maintain the well-being of tapir for long term is still required. This chapter focuses on the introduction of 16S rRNA amplicon metagenomics in analyzing Malayan tapir gut microbiome dataset.}, }
@article {pmid37258860, year = {2023}, author = {Gautam, A and Zeng, W and Huson, DH}, title = {DIAMOND + MEGAN Microbiome Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {107-131}, pmid = {37258860}, issn = {1940-6029}, abstract = {Metagenomics is the study of microbiomes using DNA sequencing technologies. Basic computational tasks are to determine the taxonomic composition (who is out there?), the functional composition (what can they do?), and also to correlate changes of composition to changes in external parameters (how do they compare?). One approach to address these issues is to first align all sequences against a protein reference database such as NCBI-nr and to then perform taxonomic and functional binning of all sequences based on their alignments. The resulting classifications can then be interactively analyzed and compared. Here we illustrate how to pursue this approach using the DIAMOND+MEGAN pipeline, on two different publicly available datasets, one containing short-read samples and other containing long-read samples.}, }
@article {pmid37258859, year = {2023}, author = {Rooney, CM and Mitra, S}, title = {A Practical Guide to 16S rRNA Microbiome Analysis in Musculoskeletal Disorders.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {85-105}, pmid = {37258859}, issn = {1940-6029}, abstract = {Microbial taxonomic assignment based on 16S marker gene amplification requires multiple data transformations, often encompassing the use of a variety of computational platforms. Bioinformatics analysis may represent a bottleneck for researchers as many tools require programmatic access in order to implement the software. Here we describe a step-by-step approach for taxonomic assignment using QIIME2 and highlight the utility of graphical-based microbiome tools for further analysis and identification of biological relevant taxa with reference to an outcome of interest.}, }
@article {pmid37258857, year = {2023}, author = {Wang, D}, title = {Metagenomics Databases for Bacteria.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {55-67}, pmid = {37258857}, issn = {1940-6029}, abstract = {The booming sequencing technologies have turned metagenomics into a widely used tool for microbe-related studies, especially in the areas of clinical medicine and ecology. Accordingly, the toolkit of metagenomics data analysis is growing stronger to provide multiple approaches for solving various biological questions and understanding the component and function of microbiome. As part of the toolkit, metagenomics databases play a central role in the creation and maintenance of processed data such as definition of taxonomic classifications, annotation of gene functions, sequence alignment, and phylogenetic tree inference. The availability of a large quantity of high-quality bacterial genomic sequences contributes significantly to the construction and update of metagenomics databases, which constitute the core resource for metagenomics data analysis at various scales. This chapter presents the key concepts, technical options, and challenges for metagenomics projects as well as the curation processes and versatile functions for the four representative bacterial metagenomics databases, including Greengenes, SILVA, Ribosomal Database Project (RDP), and Genome Taxonomy Database (GTDB).}, }
@article {pmid37258856, year = {2023}, author = {Gihawi, A and Cardenas, R and Hurst, R and Brewer, DS}, title = {Quality Control in Metagenomics Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {21-54}, pmid = {37258856}, issn = {1940-6029}, abstract = {Experiments involving metagenomics data are become increasingly commonplace. Processing such data requires a unique set of considerations. Quality control of metagenomics data is critical to extracting pertinent insights. In this chapter, we outline some considerations in terms of study design and other confounding factors that can often only be realized at the point of data analysis.In this chapter, we outline some basic principles of quality control in metagenomics, including overall reproducibility and some good practices to follow. The general quality control of sequencing data is then outlined, and we introduce ways to process this data by using bash scripts and developing pipelines in Snakemake (Python).A significant part of quality control in metagenomics is in analyzing the data to ensure you can spot relationships between variables and to identify when they might be confounded. This chapter provides a walkthrough of analyzing some microbiome data (in the R statistical language) and demonstrates a few days to identify overall differences and similarities in microbiome data. The chapter is concluded by discussing remarks about considering taxonomic results in the context of the study and interrogating sequence alignments using the command line.}, }
@article {pmid37258855, year = {2023}, author = {Benz, S and Mitra, S}, title = {From Genomics to Metagenomics in the Era of Recent Sequencing Technologies.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {1-20}, pmid = {37258855}, issn = {1940-6029}, abstract = {Metagenomics, also known as environmental genomics, is the study of the genomic content of a sample of organisms obtained from a common habitat. Metagenomics and other "omics" disciplines have captured the attention of researchers for several decades. The effect of microbes in our body is a relevant concern for health studies. Through sampling the sequences of microbial genomes within a certain environment, metagenomics allows study of the functional metabolic capacity of a community as well as its structure based upon distribution and richness of species. Exponentially increasing number of microbiome literatures illustrate the importance of sequencing techniques which have allowed the expansion of microbial research into areas, including the human gut, antibiotics, enzymes, and more. This chapter illustrates how metagenomics field has evolved with the progress of sequencing technologies.Further, from this chapter, researchers will be able to learn about all current options for sequencing techniques and comparison of their cost and read statistics, which will be helpful for planning their own studies.}, }
@article {pmid37258653, year = {2023}, author = {Garritano, AN and Majzoub, ME and Ribeiro, B and Damasceno, T and Modolon, F and Messias, C and Vilela, C and Duarte, G and Hill, L and Peixoto, R and Thomas, T}, title = {Species-specific relationships between deep sea sponges and their symbiotic Nitrosopumilaceae.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {37258653}, issn = {1751-7370}, abstract = {Sponges thrive in the deep, dark and nutrient-depleted ocean and may rely on microbial symbionts for carbon acquisition and energy generation. However, these symbiotic relationships remain largely unexplored. In this study, we analyze the microbiome of deep-sea sponges and show that ammonia-oxidizing archaea (AOA) of the family Nitrosopumilaceae make up at least 75% of the microbial communities of the sponges Aphrocallistes sp., Farrea sp. and Paratimea sp.. Given the known autotrophic metabolism of AOAs, this implies that these sponge holobionts can have the capacity for primary production in the deep-sea. We also show that specific AOA lineages are highly specific towards their hosts, hinting towards an unprecedent vertical transmission of these symbionts in deep-sea sponges. Our results show that the ecology and evolution of symbiotic relationships in deep-sea sponge is distinct from that of their shallow-water counterparts.}, }
@article {pmid37258543, year = {2023}, author = {Liu, J and Sun, J and Yu, J and Chen, H and Zhang, D and Zhang, T and Ma, Y and Zou, C and Zhang, Z and Ma, L and Yu, X}, title = {Gut microbiome determines therapeutic effects of OCA on NAFLD by modulating bile acid metabolism.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {29}, pmid = {37258543}, issn = {2055-5008}, abstract = {Non-alcoholic fatty liver disease (NAFLD), the most common chronic liver disease, had no approved pharmacological agents yet. Obeticholic acid (OCA), a novel bile acid derivative, was demonstrated to ameliorate NAFLD-related manifestations. Regarding the role of gut-liver axis in liver disease development, this study aimed to explore the potential role of gut microbiota in the treatment of OCA in NAFLD mice induced by the high-fat diet (HFD). Antibiotic-induced microbiome depletion (AIMD) and fecal microbiota transplantation (FMT) confirmed the critical role of gut microbiota in OCA treatment for NAFLD by effectively alleviating histopathological lesions and restoring liver function impaired by HFD. Metagenomic analysis indicated that OCA intervention in HFD mice remarkably increased the abundance of Akkermansia muciniphila, Bifidobacterium spp., Bacteroides spp., Alistipes spp., Lactobacillus spp., Streptococcus thermophilus, and Parasutterella excrementihominis. Targeted metabolomics analysis indicated that OCA could modulate host bile acids pool by reducing levels of serum hydrophobic cholic acid (CA) and chenodeoxycholic acid (CDCA), and increasing levels of serum-conjugated bile acids, such as taurodeoxycholic acid (TDCA) and tauroursodesoxycholic acid (TUDCA) in the HFD-fed mice. Strong correlations were observed between differentially abundant microbes and the shifted bile acids. Furthermore, bacteria enriched by OCA intervention exhibited much greater potential in encoding 7alpha-hydroxysteroid dehydrogenase (7α-HSDs) producing secondary bile acids rather than bile salt hydrolases (BSHs) mainly responsible for primary bile acid deconjugation. In conclusion, this study demonstrated that OCA intervention altered gut microbiota composition with specially enriched gut microbes modulating host bile acids, thus effectively alleviating NAFLD in the mice.}, }
@article {pmid37258525, year = {2023}, author = {Corbin, KD and Carnero, EA and Dirks, B and Igudesman, D and Yi, F and Marcus, A and Davis, TL and Pratley, RE and Rittmann, BE and Krajmalnik-Brown, R and Smith, SR}, title = {Host-diet-gut microbiome interactions influence human energy balance: a randomized clinical trial.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3161}, pmid = {37258525}, issn = {2041-1723}, abstract = {The gut microbiome is emerging as a key modulator of human energy balance. Prior studies in humans lacked the environmental and dietary controls and precision required to quantitatively evaluate the contributions of the gut microbiome. Using a Microbiome Enhancer Diet (MBD) designed to deliver more dietary substrates to the colon and therefore modulate the gut microbiome, we quantified microbial and host contributions to human energy balance in a controlled feeding study with a randomized crossover design in young, healthy, weight stable males and females (NCT02939703). In a metabolic ward where the environment was strictly controlled, we measured energy intake, energy expenditure, and energy output (fecal and urinary). The primary endpoint was the within-participant difference in host metabolizable energy between experimental conditions [Control, Western Diet (WD) vs. MBD]. The secondary endpoints were enteroendocrine hormones, hunger/satiety, and food intake. Here we show that, compared to the WD, the MBD leads to an additional 116 ± 56 kcals (P < 0.0001) lost in feces daily and thus, lower metabolizable energy for the host (89.5 ± 0.73%; range 84.2-96.1% on the MBD vs. 95.4 ± 0.21%; range 94.1-97.0% on the WD; P < 0.0001) without changes in energy expenditure, hunger/satiety or food intake (P > 0.05). Microbial 16S rRNA gene copy number (a surrogate of biomass) increases (P < 0.0001), beta-diversity changes (whole genome shotgun sequencing; P = 0.02), and fermentation products increase (P < 0.01) on an MBD as compared to a WD along with significant changes in the host enteroendocrine system (P < 0.0001). The substantial interindividual variability in metabolizable energy on the MBD is explained in part by fecal SCFAs and biomass. Our results reveal the complex host-diet-microbiome interplay that modulates energy balance.}, }
@article {pmid37258450, year = {2023}, author = {Reyes-Martínez, S and Segura-Real, L and Gómez-García, AP and Tesoro-Cruz, E and Constantino-Jonapa, LA and Amedei, A and Aguirre-García, MM}, title = {Neuroinflammation, Microbiota-Gut-Brain Axis, and Depression: The Vicious Circle.}, journal = {Journal of integrative neuroscience}, volume = {22}, number = {3}, pages = {65}, doi = {10.31083/j.jin2203065}, pmid = {37258450}, issn = {0219-6352}, abstract = {Depression is the leading cause of disability worldwide, contributing to the global disease burden. From above, it is a priority to investigate models that fully explain its physiopathology to develop new treatments. In the last decade, many studies have shown that gut microbiota (GM) dysbiosis influences brain functions and participate, in association with immunity, in the pathogenesis of depression. Thereby, GM modulation could be a novel therapeutic target for depression. This review aims to evidence how the GM and the immune system influence mental illness, particularly depression. Here, we focus on the communication mechanisms between the intestine and the brain and the impact on the development of neuroinflammation contributing to the development of Major Depressive Disorder (MDD). However, most of the current findings are in animal models, suggesting the need for studies in humans. In addition, more analysis of metabolites and cytokines are needed to identify new pathophysiological mechanisms improving anti-depression treatments.}, }
@article {pmid37258325, year = {2023}, author = {Rossi, CAM and Marchetta, EJR and Kim, JH and Castroverde, CDM}, title = {Molecular regulation of the salicylic acid hormone pathway in plants under changing environmental conditions.}, journal = {Trends in biochemical sciences}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tibs.2023.05.004}, pmid = {37258325}, issn = {0968-0004}, abstract = {Salicylic acid (SA) is a central plant hormone mediating immunity, growth, and development. Recently, studies have highlighted the sensitivity of the SA pathway to changing climatic factors and the plant microbiome. Here we summarize organizing principles and themes in the regulation of SA biosynthesis, signaling, and metabolism by changing abiotic/biotic environments, focusing on molecular nodes governing SA pathway vulnerability or resilience. We especially highlight advances in the thermosensitive mechanisms underpinning SA-mediated immunity, including differential regulation of key transcription factors (e.g., CAMTAs, CBP60g, SARD1, bHLH059), selective protein-protein interactions of the SA receptor NPR1, and dynamic phase separation of the recently identified GBPL3 biomolecular condensates. Together, these nodes form a biochemical paradigm for how the external environment impinges on the SA pathway.}, }
@article {pmid37258238, year = {2023}, author = {Togao, M and Kurakawa, T and Tajima, S and Wagai, G and Ohta-Takada, Y and Otsuka, J and Kurita, A and Kawakami, K}, title = {Human gut microbiota influences drug-metabolizing enzyme hepatic Cyp3a: A human flora-associated mice study.}, journal = {The Journal of toxicological sciences}, volume = {48}, number = {6}, pages = {333-343}, doi = {10.2131/jts.48.333}, pmid = {37258238}, issn = {1880-3989}, abstract = {Several studies revealed that gut microbiota affects the hepatic drug-metabolizing enzyme cytochrome P450 (Cyp). We hypothesized that individual gut microbiota variations could contribute to CYP activity. Human flora-associated (HFA) mice are established from germ-free mice using human feces and are often used to determine the effect of the human gut microbiota on the host. This study generated two groups of HFA mice using feces from two healthy individuals. Then, the composition of gut microbiota and hepatic Cyp activity was compared to analyze the effects of gut microbiota in healthy individuals on hepatic Cyp activity. A principal coordinate analysis based on the UniFrac distance for the composition of the cecal and fecal microbiota revealed apparent differences between the recipient groups. Hepatic Cyp, which is a marked difference in Cyp3a activity and Cyp3a11 gene expression, was observed between the recipient groups. Cyp2c and Cyp1a activities did not differ between recipient groups, with significantly lower enzymatic activities in recipients than in germ-free mice. These results indicate that the human gut microbiota affects hepatic Cyp activity. Especially, human gut microbiota composition differences have a pronounced effect on Cyp3a activity via Cyp3a11 gene expression regulation. Therefore, human gut microbiota variations among individuals may affect numerous drug metabolism, leading to drug efficacy and toxicity.}, }
@article {pmid37257865, year = {2023}, author = {Favale, N and Farina, R and Carrieri, A and Simonelli, A and Severi, M and Sabbioni, S and Trombelli, L and Scapoli, C}, title = {Functional profile of oral plaque microbiome: Further insight into the bidirectional relationship between type 2 diabetes and periodontitis.}, journal = {Molecular oral microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/omi.12418}, pmid = {37257865}, issn = {2041-1014}, abstract = {Increasing evidence support the association between the oral microbiome and human systemic diseases. This association may be attributed to the ability of many oral microbes to influence the inflammatory microenvironment. Herein, we focused our attention on the bidirectional relationship between periodontitis and type 2 diabetes using high-resolution whole metagenomic shotgun analysis to explore the composition and functional profile of the subgingival microbiome in diabetics and non-diabetics subjects with different periodontal conditions. In the present study, the abundance of metabolic pathways encoded by oral microbes was reconstructed from the metagenome, and we identified a set of dysregulated metabolic pathways significantly enriched in the periodontitis and/or diabetic patients. These pathways were mainly involved in branched and aromatic amino acids metabolism, fatty acid biosynthesis and adipocytokine signaling pathways, ferroptosis and iron homeostasis, nucleotide metabolism, and finally in the peptidoglycan and lipopolysaccharides synthesis. Overall, the results of the present study provide evidence in favor of the hypothesis that during the primary inflammatory challenge, regardless of whether it is induced by periodontitis or diabetes, endotoxemia and/or the release of inflammatory cytokines cause a change in precursor and/or in circulating innate immune cells. Dysbiosis and inflammation, also via oral-gut microbiome axis or adipose tissue, reduce the efficacy of the host immune response, while fueling inflammation and can induce that metabolic/epigenetic reprogramming of chromatin accessibility of genes related to the immune response. Moreover, the presence of an enhanced ferroptosis and an imbalance in purine/pyrimidine metabolism provides new insights into the role of ferroptotic death in this comorbidity.}, }
@article {pmid37257737, year = {2023}, author = {Chatterjee, K and Mazumder, PM and Sarkar, SR and Saha, R and Chatterjee, A and Sarkar, B and Banerjee, S}, title = {Neuroprotective effect of Vitamin K2 against gut dysbiosis associated cognitive decline.}, journal = {Physiology &amp; behavior}, volume = {}, number = {}, pages = {114252}, doi = {10.1016/j.physbeh.2023.114252}, pmid = {37257737}, issn = {1873-507X}, abstract = {Vitamin K2/ Menaquinones produced predominantly by the gut microbiome improve bone health and prevent coronary calcification. The central nervous system has been linked with gut microbiota via the gut-brain axis and is strongly associated with psychiatric conditions. In the present study, we show the role of Vitamin K2 (MK-7) in gut dysbiosis-associated cognitive decline. Gut dysbiosis was induced in mice by administering Ampicillin (250 mg/kg twice a day orally) for 14 days and Vitamin K2 (0.05 mg/kg) for 21 days with or without antibiotic treatment and altered gene expression profile of intestinal microbes determined. This was followed by behavioural studies to determine cognitive changes. The behavioural observations are then correlated with proinflammatory, oxidative, and brain and intestinal histopathological changes in antibiotic-treated animals with or without vitamin K2 administration. With the use of antibiotics, Lactobacillus, Bifidobacterium, Firmicutes, and Clostridium's relative abundance reduced. When vitamin K2 was added to the medication, their levels were restored. Cognitive impairment was observed in behavioural trials in the antibiotic group, but this drop was restored in mice given both an antibiotic and vitamin K. Myeloperoxidase levels in the colon and brain increased due to gut dysbiosis, which vitamin K2 prevented. The acetylcholine esterase and oxidative stress markers brought on by antibiotics were also decreased by vitamin K2. Additionally, vitamin K2 guarded against alterations in intestine ultrastructure brought on by antibiotic use and preserved hippocampus neurons. So, it can be concluded that vitamin K2 improved cognitive skills, avoided hippocampus neuronal damage from antibiotics, and lowered intestine and brain inflammation and oxidative stress.}, }
@article {pmid37257731, year = {2023}, author = {Szukala, W and Pilarczyk-Zurek, M and Folkert, J and Kotlinowski, J and Koziel, J and Jura, J}, title = {Depletion of Mcpip1 in murine myeloid cells results in intestinal dysbiosis followed by allergic inflammation.}, journal = {Biochimica et biophysica acta. Molecular basis of disease}, volume = {}, number = {}, pages = {166764}, doi = {10.1016/j.bbadis.2023.166764}, pmid = {37257731}, issn = {1879-260X}, abstract = {MCPIP1 (called also Regnase-1) is a negative regulator of inflammation. Knockout of the Zc3h12a gene, encoding Mcpip1 in cells of myeloid origin (Mcpip1[MKO]), has a pathological effect on many organs. The aim of this study was to comprehensively analyze pathological changes in the skin caused by Mcpip1 deficiency in phagocytes with an emphasis on its molecular mechanism associated with microbiome dysbiosis. Mcpip1[MKO] mice exhibited spontaneous wound formation on the skin. On a molecular level, the Th2-type immune response was predominantly characterized by an increase in Il5 and Il13 transcript levels, as well as eosinophil and mast cell infiltration. Irritation by DNFB led to a more severe skin contact allergy in Mcpip1[MKO] mice. Allergic reactions on the skin were strongly influenced by gut dysbiosis and enhanced systemic dissemination of bacteria. This process was followed by activation of the C/EBP pathway in peripheral macrophages, leading to local changes in the cytokine microenvironment that promoted the Th2 response. A reduced bacterial load inhibited allergic inflammation, indicating the role of intestinal dysbiosis in the development of skin diseases. Our results clearly show that MCPIP1 in phagocytes is an essential negative regulator that controls the gut-skin axis.}, }
@article {pmid37257548, year = {2023}, author = {Ogunkolade, W and Senusi, AA and Desai, P and Sacoor, S and Bibi, A and Gokani, B and Sandionigi, A and Fortune, F}, title = {Profiling the microbiome of oral and genital mucosal surfaces in Behçet's disease.}, journal = {Clinical immunology (Orlando, Fla.)}, volume = {}, number = {}, pages = {109654}, doi = {10.1016/j.clim.2023.109654}, pmid = {37257548}, issn = {1521-7035}, abstract = {UNLABELLED: Almost 90% of Behçet's patients present with oral and/or genital ulcers which influence the disease outcome. We hypothesised that the dysregulation of the oral and genital microbiome, coupled with dysregulation of the immune response, contributes to the aetiopathogenesis of Behçet's Disease (BD) and drives disease activation.<br><br>METHOD: 152 BD patient samples; 70 matched oral and genital samples plus 12 unmatched samples (Female: Male, 58:12; mean age, 42&#x202f;&#xb1;&#x202f;13.9: 39.3&#x202f;&#xb1;&#x202f;10.3) to profile microbial community high-throughput sequencing of the microbiome using 16&#x202f;s rRNA sequencing targeting the V1/V2 and V3/V4 hyper variable regions were used and results reviewed in relation to disease severity, Work and Social Adjustment Scale (WSAS) outcomes and medication.<br><br>RESULTS: Alpha and beta diversity were significantly decreased in genital compared to oral samples; p value<0.05. However, grouping the samples as to whether ulceration was present was not significant. Escherichia-Shigella was the only Amplicon Sequence Variants (ASVs) in the V1/V2 region that was shared between the oral mucosa with ulcer (O_U) and genital mucosa with ulcer (G_U) groups. This was in contrast to the V3/V4 region which indicated that Lachnospiraceae, Saccharimonadales, and Coriobacteriales were shared between the O_U and G_U groups. In addition, gender had no impact on the bacterial abundance in V1/V2 analysis of the oral and genital samples. V3/V4 analysis of genital samples demonstrated that Lactobacilli and Gardnerella were significantly increased in females (20 times) compared to the males in samples; p-adj <0.05. Interestingly in BD patients, Rothia which is commonly found in the mouth was present in both oral and genital samples. Streptococci were significantly increased while Veillonella significantly decreased in the presence of oral ulceration in the BD cohort. The clinical phenotype had no effect on V1/V2 and V3/V4 on the bacterial abundance of oral samples. However, medication e.g. colchicine had a significant effect on the oral microbial abundance (V1/V2; P&#x202f;=&#x202f;0.020, V3/V4; P&#x202f;=&#x202f;0.003). There was no relationship between colchicine and the presence/absence of genital ulcers. BD patients with active disease had higher WSAS scores, and their bacterial abundance differed significantly from the non-active BD patients (ADONIS, R2&#x202f;=&#x202f;0.05, p value =0.029).<br><br>CONCLUSION: The presence of the microbes Streptococcus, Veillonella, Gardnerella, Lactobacillus, Atopobium, Peptoniphilus, Corynebacterium and Staphylococcus may provide early evidence of BD patients are with active disease.}, }
@article {pmid37257501, year = {2023}, author = {Osorio-Doblado, AM and Feldmann, KP and Lourenco, JM and Stewart, RL and Smith, WB and Tedeschi, LO and Fluharty, FL and Callaway, TR}, title = {Forages and Pastures Symposium: Forage biodegradation: Advances in ruminal microbial ecology.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skad178}, pmid = {37257501}, issn = {1525-3163}, abstract = {The rumen microbial ecosystem provides ruminants a selective advantage, the ability to utilize forages, allowing them to flourish worldwide in various environments. For many years, our understanding of the ruminal microbial ecosystem was limited to understanding the microbes (usually only laboratory-amenable bacteria) grown in pure culture, meaning that much of our understanding of ruminal function remained a "black box." However, the ruminal degradation of plant cell walls is performed by a consortium of bacteria, archaea, protozoa, and fungi that produces a wide variety of carbohydrate active enzymes (CAZymes) that are responsible for the catabolism of cellulose, hemicellulose, and pectin. The past 15 years have seen the development and implementation of numerous next-generation sequencing (NGS) approaches (e.g., pyrosequencing, Illumina, and shotgun sequencing), which have contributed significantly to a greater level of insight regarding the microbial ecology of ruminants fed a variety of forages. There has also been an increase in the utilization of liquid chromatography (LC) and mass spectrometry (MS) that revolutionized transcriptomic approaches, and further improvements in the measurement of fermentation intermediates and end products have advanced with metabolomics. These advanced NGS techniques along with other analytic approaches, such as metaproteomics, have been utilized to elucidate the specific role of microbial CAZymes in forage degradation. Other methods have provided new insights into dynamic changes in the ruminal microbial population fed different diets and how these changes impact the assortment of products presented to the host animal. As more omics-based data has accumulated on forage-fed ruminants, the sequence of events that occur during fiber colonization by the microbial consortium has become more apparent, with fungal populations and fibrolytic bacterial populations working in conjunction, as well as expanding understanding of the individual microbial contributions to degradation of plant cell walls and polysaccharide components. In the future, the ability to predict microbial population and enzymatic activity and end products will be able to support the development of dynamic predictive models of rumen forage degradation and fermentation. Consequently, it is imperative to understand the rumen's microbial population better to improve fiber degradation in ruminants and, thus, stimulate more sustainable production systems.}, }
@article {pmid37257477, year = {2023}, author = {Schönherr, S and Jung, L and Lübbert, C}, title = {[Clostridioides difficile - New Insights and Therapy Recommendations].}, journal = {Deutsche medizinische Wochenschrift (1946)}, volume = {148}, number = {12}, pages = {752-758}, doi = {10.1055/a-1970-9211}, pmid = {37257477}, issn = {1439-4413}, abstract = {After an increase in Clostridioides difficile infections (CDI) until 2013 due to epidemic ribotypes such as 027 and 078, CDI incidence in Germany is now declining, as confirmed by recent epidemiological data. Despite this success through antimicrobial stewardship and hospital hygiene, the burden of disease remains high, especially in older patients (>65 years) with comorbidities. The main risk factor for CDI is the use of broad-spectrum antibiotics, which disrupt the gut microbiota, allowing C. difficile colonization. Coinfection with other intestinal pathogens such as enterococci can further increase the virulence of C. difficile. The updated 2021 ESCMID guidelines recommend fidaxomicin instead of vancomycin as the antibiotic of choice for the treatment of CDI because of its lower recurrence rate. Vancomycin remains a good alternative; however, metronidazole should only be used if neither antibiotic is available. In the future, ridinilazole may be available as another therapeutic option that has a narrow spectrum of activity and low intestinal absorption. For the treatment of recurrent CDI, the new guidelines also include the use of the monoclonal antibody bezlotoxumab. In addition, a new oral microbiome therapy, SER-109 (capsules containing purified Firmicutes spores), which showed promising results in a phase 3 study, may provide an easy-to-administer alternative to fecal microbiota transplantation. Hopes for a well-performing toxoid vaccine for primary and secondary prevention of CDI have unfortunately not been fulfilled in the CLOVER trial.}, }
@article {pmid37257346, year = {2023}, author = {Xu, L and Wang, R and Jin, B and Chen, J and Jiang, T and Ali, W and Tian, S and Lu, L}, title = {Cadmium inhibits powdery mildew colonization and reconstructs microbial community in leaves of the hyperaccumulator plant Sedum alfredii.}, journal = {Ecotoxicology and environmental safety}, volume = {260}, number = {}, pages = {115076}, doi = {10.1016/j.ecoenv.2023.115076}, pmid = {37257346}, issn = {1090-2414}, abstract = {Understanding the influence of the heavy metal cadmium (Cd) on the phyllosphere microbiome of hyperaccumulator plants is crucial for enhancing phytoremediation. The characteristics of the phyllosphere of Sedum alfredii Hance, a hyperaccumulator plant, were investigated using 16S rRNA and internal transcribed spacer amplicon sequencing of powdery mildew-infected leaves treated or untreated with Cd. The results showed that the colonization of powdery mildew caused severe chlorosis and necrosis in S. alfredii leaves, and the relative abundance of Leotiomycetes in infected leaves increased dramatically and significantly decreased phyllosphere microbiome diversity. However, S. alfredii preferentially accumulated higher concentrations of Cd in the leaves of infected plants than in uninfected plants by powdery mildew, which in turn significantly inhibited powdery mildew colonization in leaves; the relative abundance of the fungal class Leotiomycetes in infected leaves decreased, and alpha and beta diversities of the phyllosphere microbiome significantly increased with Cd treatment in the infected plants. In addition, the inter-kingdom networks in the microbiota of the infected leaves treated with Cd presented many nodes and edges, and the highest inter-kingdom modularity compared to the untreated infected leaves, indicating a highly connected microbial community. These results suggest that Cd significantly inhibits powdery mildew colonization by altering the composition of the phyllosphere microbiome in S. alfredii leaves, paving the way for efficient heavy metal phytoremediation and providing a new perspective on defense strategies against heavy metals.}, }
@article {pmid37256894, year = {2023}, author = {Matheri, F and Kambura, AK and Mwangi, M and Karanja, E and Adamtey, N and Wanjau, K and Mwangi, E and Tanga, CM and Bautze, D and Runo, S}, title = {Evolution of fungal and non-fungal eukaryotic communities in response to thermophilic co-composting of various nitrogen-rich green feedstocks.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0286320}, doi = {10.1371/journal.pone.0286320}, pmid = {37256894}, issn = {1932-6203}, abstract = {Thermophilic composting is a promising soil and waste management approach involving diverse micro and macro-organisms, including eukaryotes. Due to sub-optimal amounts of nutrients in manure, supplemental feedstock materials such as Lantana camara, and Tithonia diversifolia twigs are used in composting. These materials have, however, been reported to have antimicrobial activity in in-vitro experiments. Furthermore, the phytochemical analysis has shown differences in their complexities, thus possibly requiring various periods to break down. Therefore, it is necessary to understand these materials' influence on the biological and physical-chemical stability of compost. Most compost microbiome studies have been bacterial-centric, leaving out eukaryotes despite their critical role in the environment. Here, the influence of different green feedstock on the fungal and non-fungal eukaryotic community structure in a thermophilic compost environment was examined. Total community fungal and non-fungal eukaryotic DNA was recovered from triplicate compost samples of four experimental regimes. Sequencing for fungal ITS and non-fungal eukaryotes; 18S rDNA was done under the Illumina Miseq platform, and bioinformatics analysis was done using Divisive Amplicon Denoising Algorithm version 2 workflow in R version 4.1. Samples of mixed compost and composting day 84 recorded significantly (P<0.05) higher overall fungal populations, while Lantana-based compost and composting day 84 revealed the highest fungal community diversity. Non-fungal eukaryotic richness was significantly (P< 0.05) more abundant in Tithonia-based compost and composting day 21. The most diverse non-fungal eukaryotic biome was in the Tithonia-based compost and composting day 84. Sordariomycetes and Holozoa were the most contributors to the fungal and non-fungal community interactions in the compost environment, respectively. The findings of this study unravel the inherent influence of diverse composting materials and days on the eukaryotic community structure and compost's biological and chemical stability.}, }
@article {pmid37256822, year = {2023}, author = {Tournay, RJ and Firrincieli, A and Parikh, SS and Sivitilli, DM and Doty, SL}, title = {Effect of Arsenic on EPS Synthesis, Biofilm Formation, and Plant Growth-Promoting Abilities of the Endophytes Pseudomonas PD9R and Rahnella laticis PD12R.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.2c08586}, pmid = {37256822}, issn = {1520-5851}, abstract = {Phytoremediation, a cost-effective, eco-friendly alternative to conventional remediation, could expand efforts to remediate arsenic-contaminated soils. As with other pollutants, the plant microbiome may improve phytoremediation outcomes for arsenic-contaminated sites. We used in vitro and in silico methods to compare the arsenic resistance mechanisms, synthesis of extracellular polymeric substances (EPS), biofilm formation, and plant growth-promoting abilities of the endophytes Pseudomonas sp. PD9R and Rahnella laticis PD12R. PD12R, which tolerates arsenate (As(V)) and arsenite (As(III)) to concentrations fivefold greater than PD9R, synthesizes high volumes of EPS in response to arsenic, and sequesters arsenic in the capsular EPS and cells. While arsenic exposure induced EPS synthesis in both strains, only PD12R continued to form biofilms at high As(III) and As(V) concentrations. The effects of endophyte inoculation on Arabidopsis growth varied by strain and As(V) concentration, and PD9R had positive effect on plants exposed to low levels of arsenic. Comparative genomic analyses exploring the EPS synthesis and arsenic resistance mechanisms against other Pseudomonas and Rahnella strains suggest that both strains possess atypical arsenic resistance mechanisms from other plant-associated strains, while the configuration of the EPS synthesis systems appeared to be more broadly distributed among plant- and non-plant-associated strains.}, }
@article {pmid37256194, year = {2023}, author = {Salia, S and Martin, Y and Burke, FF and Myles, LA and Jackman, L and Halievski, K and Bambico, FR and Swift-Gallant, A}, title = {Antibiotic-induced socio-sexual behavioral deficits are reversed via cecal microbiota transplantation but not androgen treatment.}, journal = {Brain, behavior, &amp; immunity - health}, volume = {30}, number = {}, pages = {100637}, pmid = {37256194}, issn = {2666-3546}, abstract = {Recent evidence has demonstrated a sex-specific role of the gut microbiome on social behavior such as anxiety, possibly driven by a reciprocal relationship between the gut microbiome and gonadal hormones. For instance, gonadal hormones drive sex differences in gut microbiota composition, and certain gut bacteria can produce androgens from glucocorticoids. We thus asked whether the gut microbiome can influence androgen-dependent socio-sexual behaviors. We first treated C57BL/6 mice with broad-spectrum antibiotics (ABX) in drinking water to deplete the gut microbiota either transiently during early development (embryonic day 16-postnatal day [PND] 21) or in adulthood (PND 60-85). We hypothesized that if ABX interferes with androgens, then early ABX would interfere with critical periods for sexual differentiation of brain and thus lead to long-term decreases in males' socio-sexual behavior, while adult ABX would interfere with androgens' activational effects on behavior. We found that in males but not females, early and adult ABX treatment decreased territorial aggression, and adult ABX also decreased sexual odor preference. We then assessed whether testosterone and/or cecal microbiota transplantation (CMT) via oral gavage could prevent ABX-induced socio-sexual behavioral deficits in adult ABX-treated males. Mice were treated with same- or other-sex control cecum contents or with testosterone for two weeks. While testosterone was not effective in rescuing any behavior, we found that male CMT restored both olfactory preference and aggression in adult ABX male mice, while female CMT restored olfactory preference but not aggression. These results suggest sex-specific effects of the gut microbiome on socio-sexual behaviors, independent of androgens.}, }
@article {pmid37256150, year = {2023}, author = {Ben-Azu, B and Del Re, EC and VanderZwaag, J and Carrier, M and Keshavan, M and Khakpour, M and Tremblay, M&#xc8;}, title = {Emerging epigenetic dynamics in gut-microglia brain axis: experimental and clinical implications for accelerated brain aging in schizophrenia.}, journal = {Frontiers in cellular neuroscience}, volume = {17}, number = {}, pages = {1139357}, pmid = {37256150}, issn = {1662-5102}, abstract = {Brain aging, which involves a progressive loss of neuronal functions, has been reported to be premature in probands affected by schizophrenia (SCZ). Evidence shows that SCZ and accelerated aging are linked to changes in epigenetic clocks. Recent cross-sectional magnetic resonance imaging analyses have uncovered reduced brain reserves and connectivity in patients with SCZ compared to typically aging individuals. These data may indicate early abnormalities of neuronal function following cyto-architectural alterations in SCZ. The current mechanistic knowledge on brain aging, epigenetic changes, and their neuropsychiatric disease association remains incomplete. With this review, we explore and summarize evidence that the dynamics of gut-resident bacteria can modulate molecular brain function and contribute to age-related neurodegenerative disorders. It is known that environmental factors such as mode of birth, dietary habits, stress, pollution, and infections can modulate the microbiota system to regulate intrinsic neuronal activity and brain reserves through the vagus nerve and enteric nervous system. Microbiota-derived molecules can trigger continuous activation of the microglial sensome, groups of receptors and proteins that permit microglia to remodel the brain neurochemistry based on complex environmental activities. This remodeling causes aberrant brain plasticity as early as fetal developmental stages, and after the onset of first-episode psychosis. In the central nervous system, microglia, the resident immune surveillance cells, are involved in neurogenesis, phagocytosis of synapses and neurological dysfunction. Here, we review recent emerging experimental and clinical evidence regarding the gut-brain microglia axis involvement in SCZ pathology and etiology, the hypothesis of brain reserve and accelerated aging induced by dietary habits, stress, pollution, infections, and other factors. We also include in our review the possibilities and consequences of gut dysbiosis activities on microglial function and dysfunction, together with the effects of antipsychotics on the gut microbiome: therapeutic and adverse effects, role of fecal microbiota transplant and psychobiotics on microglial sensomes, brain reserves and SCZ-derived accelerated aging. We end the review with suggestions that may be applicable to the clinical setting. For example, we propose that psychobiotics might contribute to antipsychotic-induced therapeutic benefits or adverse effects, as well as reduce the aging process through the gut-brain microglia axis. Overall, we hope that this review will help increase the understanding of SCZ pathogenesis as related to chronobiology and the gut microbiome, as well as reveal new concepts that will serve as novel treatment targets for SCZ.}, }
@article {pmid37256109, year = {2023}, author = {Rui, X and Fu, Y and Cai, J and Zhang, Y and Fu, Q and He, C}, title = {Gut microbiota were altered with platelet count and red blood cell count in immune thrombocytopenia patients with different treatments.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1168756}, pmid = {37256109}, issn = {2235-2988}, abstract = {The gut microbiome is clearly linked to the development of various autoimmune diseases, however, its association with immune thrombocytopenia (ITP) is less well understood. The current study collected 73 samples, including 36 from healthy individuals and 37 from ITP patients. The gut microbial community was assessed using 16s rRNA sequencing. Findings illustrated that the abundance of key microbiota was significantly higher in the ITP group. This group was further divided into three subgroups that received different treatments for ITP. A random forest model was used to predict the key microbiota and the identified bacteria were shown to easily distinguish between the healthy and the ITP treatment groups. Microbial function annotation and difference analysis showed that drug treatment changed the gut microbiota and may play a role in inducing host autoimmune responses by changing microbial metabolism pathways. Clinical indices also correlated negatively with changes in the microbiota after treatment. In summary, ITP patients who received drug treatment had significant differences in their microbiota along with a high abundance of bacteria. Thus, the microbiome could be used as a biomarker to distinguish between healthy and ITB groups. The key differential bacteria could help to regulate the number of platelets in ITP patients and provide a red blood cell overstock.}, }
@article {pmid37256066, year = {2023}, author = {Han, W and Ye, Z and Gu, Y and Zhong, Y and Gao, J and Zhao, S and Wang, S}, title = {Gut microbiota composition and gene expression changes induced in the Apis cerana exposed to acetamiprid and difenoconazole at environmentally realistic concentrations alone or combined.}, journal = {Frontiers in physiology}, volume = {14}, number = {}, pages = {1174236}, pmid = {37256066}, issn = {1664-042X}, abstract = {Apis cerana is an important pollinator of agricultural crops in China. In the agricultural environment, A. cerana may be exposed to acetamiprid (neonicotinoid insecticide) and difenoconazole (triazole fungicide), alone or in combination because they are commonly applied to various crops. At present, our understanding of the toxicological effects of acetamiprid and difenoconazole on honey bee gut microbiomes is limited. The primary objective of this study was to explore whether these two pesticides affect honey bees' gut microbiota and to analyze the transcriptional effects of these two pesticides on honey bees' head and gut. In this study, adults of A. cerana were exposed to acetamiprid and/or difenoconazole by contaminated syrup at field-realistic concentrations for 10 days. Results indicated that acetamiprid and/or difenoconazole chronic exposure did not affect honey bees' survival and food consumption, whereas difenoconazole decreased the weight of honey bees. 16S rRNA sequencing suggested that difenoconazole and the mixture of difenoconazole and acetamiprid decreased the diversity index and shaped the composition of gut bacteria microbiota, whereas acetamiprid did not impact the gut bacterial community. The ITS sequence data showed that neither of the two pesticides affected the fungal community structure. Meanwhile, we also observed that acetamiprid or difenoconazole significantly altered the expression of genes related to detoxification and immunity in honey bees' tissues. Furthermore, we observed that the adverse effect of the acetamiprid and difenoconazole mixture on honey bees' health was greater than that of a single mixture. Taken together, our study demonstrates that acetamiprid and/or difenoconazole exposure at field-realistic concentrations induced changes to the honey bee gut microbiome and gene expression.}, }
@article {pmid37256058, year = {2023}, author = {Saqib, HSA and Sun, L and Pozsgai, G and Liang, P and Goraya, MU and Akutse, KS and You, M and Gurr, GM and You, S}, title = {Gut microbiota assemblages of generalist predators are driven by local- and landscape-scale factors.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1172184}, pmid = {37256058}, issn = {1664-302X}, abstract = {The gut microbiomes of arthropods have significant impact on key physiological functions such as nutrition, reproduction, behavior, and health. Spiders are diverse and numerically dominant predators in crop fields where they are potentially important regulators of pests. Harnessing spiders to control agricultural pests is likely to be supported by an understanding of their gut microbiomes, and the environmental drivers shaping microbiome assemblages. This study aimed to deciphering the gut microbiome assembly of these invertebrate predators and elucidating potential implications of key environmental constraints in this process. Here, we used high-throughput sequencing to examine for the first time how the assemblages of bacteria in the gut of spiders are shaped by environmental variables. Local drivers of microbiome composition were globally-relevant input use system (organic production vs. conventional practice), and crop identity (Chinese cabbage vs. cauliflower). Landscape-scale factors, proportion of forest and grassland, compositional diversity, and habitat edge density, also strongly affected gut microbiota. Specific bacterial taxa were enriched in gut of spiders sampled from different settings and seasons. These findings provide a comprehensive insight into composition and plasticity of spider gut microbiota. Understanding the temporal responses of specific microbiota could lead to innovative strategies development for boosting biological control services of predators.}, }
@article {pmid37256051, year = {2023}, author = {Cha, T and Kim, HH and Keum, J and Kwak, MJ and Park, JY and Hoh, JK and Kim, CR and Jeon, BH and Park, HK}, title = {Gut microbiome profiling of neonates using Nanopore MinION and Illumina MiSeq sequencing.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1148466}, pmid = {37256051}, issn = {1664-302X}, abstract = {This study aimed to evaluate the difference in gut microbiomes between preterm and term infants using third-generation long-read sequencing (Oxford Nanopore Technologies, ONT) compared with an established gold standard, Illumina (second-generation short-read sequencing). A total of 69 fecal samples from 51 term (T) and preterm (P) infants were collected at 7 and 28 days of life. Gut colonization profiling was performed by 16S rRNA gene sequencing using ONT. We used Illumina to validate and compare the patterns in 13 neonates. Using bioinformatic analysis, we identified features that differed between P and T. Both T1 and P1 microbiomes were dominated by Firmicutes (Staphylococcus and Enterococcus), whereas sequentially showed dominant transitions to Lactobacillus (p < 0.001) and Streptococcus in T2 (p = 0.001), and pathogenic bacteria (Klebsiella) in P2 (p = 0.001). The abundance of beneficial bacteria (Bifidobacterium and Lactobacillus) increased in T2 (p = 0.026 and p < 0.001, respectively). These assignments were correlated with the abundance at the species-level. Bacterial α-diversity increased in T (p = 0.005) but not in P (p = 0.156), and P2 showed distinct β-diversity clustering than T2 (p = 0.001). The ONT reliably identified pathogenic bacteria at the genus level, and taxonomic profiles were comparable to those identified by Illumina at the genus level. This study shows that ONT and Illumina are highly correlated. P and T had different microbiome profiles, and the α- and β-diversity varied. ONT sequencing has potential for pathogen detection in neonates in clinical settings.}, }
@article {pmid37256048, year = {2023}, author = {Yousefi, B and Melograna, F and Galazzo, G and van Best, N and Mommers, M and Penders, J and Schwikowski, B and Van Steen, K}, title = {Capturing the dynamics of microbial interactions through individual-specific networks.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1170391}, pmid = {37256048}, issn = {1664-302X}, abstract = {Longitudinal analysis of multivariate individual-specific microbiome profiles over time or across conditions remains dauntin. Most statistical tools and methods that are available to study microbiomes are based on cross-sectional data. Over the past few years, several attempts have been made to model the dynamics of bacterial species over time or across conditions. However, the field needs novel views on handling microbial interactions in temporal analyses. This study proposes a novel data analysis framework, MNDA, that combines representation learning and individual-specific microbial co-occurrence networks to uncover taxon neighborhood dynamics. As a use case, we consider a cohort of newborns with microbiomes available at 6 and 9 months after birth, and extraneous data available on the mode of delivery and diet changes between the considered time points. Our results show that prediction models for these extraneous outcomes based on an MNDA measure of local neighborhood dynamics for each taxon outperform traditional prediction models solely based on individual-specific microbial abundances. Furthermore, our results show that unsupervised similarity analysis of newborns in the study, again using the notion of a taxon's dynamic neighborhood derived from time-matched individual-specific microbial networks, can reveal different subpopulations of individuals, compared to standard microbiome-based clustering, with potential relevance to clinical practice. This study highlights the complementarity of microbial interactions and abundances in downstream analyses and opens new avenues to personalized prediction or stratified medicine with temporal microbiome data.}, }
@article {pmid37255938, year = {2023}, author = {Hasegawa, Y and Kim, DHJ and Zhang, Z and Taha, AY and Capitanio, JP and Hogrefe, CE and Bauman, MD and Golub, MS and Van de Water, J and VandeVoort, CA and Walker, CK and Slupsky, CM}, title = {Calorie restriction and pravastatin administration during pregnancy in obese rhesus macaques modulates maternal and infant metabolism and infant brain and behavioral development.}, journal = {Frontiers in nutrition}, volume = {10}, number = {}, pages = {1146804}, pmid = {37255938}, issn = {2296-861X}, abstract = {BACKGROUND: Maternal obesity has been associated with a higher risk of pregnancy-related complications in mothers and offspring; however, effective interventions have not yet been developed. We tested two interventions, calorie restriction and pravastatin administration, during pregnancy in a rhesus macaque model with the hypothesis that these interventions would normalize metabolic dysregulation in pregnant mothers leading to an improvement in infant metabolic and cognitive/social development.<br><br>METHODS: A total of 19 obese mothers were assigned to either one of the two intervention groups (n&#x2009;=&#x2009;5 for calorie restriction; n&#x2009;=&#x2009;7 for pravastatin) or an obese control group (n&#x2009;=&#x2009;7) with no intervention, and maternal gestational samples and postnatal infant samples were compared with lean control mothers (n&#x2009;=&#x2009;6) using metabolomics methods.<br><br>RESULTS: Gestational calorie restriction normalized one-carbon metabolism dysregulation in obese mothers, but altered energy metabolism in her offspring. Although administration of pravastatin during pregnancy tended to normalize blood cholesterol in the mothers, it potentially impacted the gut microbiome and kidney function of their offspring. In the offspring, both calorie restriction and pravastatin administration during pregnancy tended to normalize the activity of AMPK in the brain at 6 months, and while results of the Visual Paired-Comparison test, which measures infant recognition memory, was not significantly impacted by either of the interventions, gestational pravastatin administration, but not calorie restriction, tended to normalize anxiety assessed by the Human Intruder test.<br><br>CONCLUSIONS: Although the two interventions tested in a non-human primate model led to some improvements in metabolism and/or infant brain development, negative impacts were also found in both mothers and infants. Our study emphasizes the importance of assessing gestational interventions for maternal obesity on both maternal and offspring long-term outcomes.}, }
@article {pmid37255660, year = {2023}, author = {Kaune, T and Griesmann, H and Theuerkorn, K and Hämmerle, M and Laumen, H and Krug, S and Plumeier, I and Kahl, S and Junca, H and Gustavo Dos Anjos Borges, L and Michl, P and Pieper, DH and Rosendahl, J}, title = {Gender-specific changes of the gut microbiome correlate with tumor development in murine models of pancreatic cancer.}, journal = {iScience}, volume = {26}, number = {6}, pages = {106841}, pmid = {37255660}, issn = {2589-0042}, abstract = {Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with a dismal outcome. To improve understanding of sequential microbiome changes during PDAC development we analyzed mouse models of pancreatic carcinogenesis (KC mice recapitulating pre-invasive PanIN formation, as well as KPC mice recapitulating invasive PDAC) during early tumor development and subsequent tumor progression. Diversity and community composition were analyzed depending on genotype, age, and gender. Both mouse models demonstrated concordant abundance changes of several genera influenced by one or more of the investigated factors. Abundance was significantly impacted by gender, highlighting the need to further elucidate the impact of gender differences. The findings underline the importance of the microbiome in PDAC development and indicate that microbiological screening of patients at risk and targeting the microbiome in PDAC development may be feasible in future.}, }
@article {pmid37255542, year = {2023}, author = {Raith, M and Swoboda, I}, title = {Birch pollen-The unpleasant herald of spring.}, journal = {Frontiers in allergy}, volume = {4}, number = {}, pages = {1181675}, pmid = {37255542}, issn = {2673-6101}, abstract = {Type I respiratory allergies to birch pollen and pollen from related trees of the order Fagales are increasing in industrialized countries, especially in the temperate zone of the Northern hemisphere, but the reasons for this increase are still debated and seem to be multifaceted. While the most important allergenic molecules of birch pollen have been identified and characterized, the contribution of other pollen components, such as lipids, non-allergenic immunomodulatory proteins, or the pollen microbiome, to the development of allergic reactions are sparsely known. Furthermore, what also needs to be considered is that pollen is exposed to external influences which can alter its allergenicity. These external influences include environmental factors such as gaseous pollutants like ozone or nitrogen oxides or particulate air pollutants, but also meteorological events like changes in temperature, humidity, or precipitation. In this review, we look at the birch pollen from different angles and summarize current knowledge on internal and external influences that have an impact on the allergenicity of birch pollen and its interactions with the epithelial barrier. We focus on epithelial cells since these cells are the first line of defense in respiratory disease and are increasingly considered to be a regulatory tissue for the protection against the development of respiratory allergies.}, }
@article {pmid37255465, year = {2023}, author = {Katati, B and Schoenmakers, P and Njapau, H and Kachapulula, PW and Zwaan, BJ and van Diepeningen, AD and Schoustra, SE}, title = {Preharvest Maize Fungal Microbiome and Mycotoxin Contamination: Case of Zambia's Different Rainfall Patterns.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0007823}, doi = {10.1128/aem.00078-23}, pmid = {37255465}, issn = {1098-5336}, abstract = {The preharvest maize mycobiome may be crucial in defining the health of the crop in terms of potential disease burden and mycotoxins. We investigated the preharvest maize mycobiome structure, including the influence of weather patterns, in terms of rainfall intensity, on its composition. In addition, we investigated correlation of genera Fusarium and Aspergillus with maize fumonisin-B1 and aflatoxin. Forty maize fields from selected districts in the wetter northern (N) and drier southern (S) agroecological zones of Zambia were sampled twice over two seasons (1 and 2). The defined weather variables over the two seasons were low rainfall with dry spell (S1), low rainfall (S2), and high rainfall (N1 and N2). High-throughput DNA amplicon sequencing of internal transcribed spacer 1 (ITS1) was used to determine the mycobiome structure and the composition in relation to rainfall patterns. We detected 61 genera, with Fusarium and previously unreported Sarocladium in Zambia to have the highest frequency of detection on the maize. There was a significant difference in fungal genera composition between S1 and S2 but no difference between N1 and N2. The weather pattern with dry spell, S1, had a strong proliferation of Meyerozyma and xerophiles Penicillium, Kodamaea, and Aspergillus. The four genera drove the difference in composition between S1 and S2 and the significantly higher fungal diversity in S1 compared to N2. Of the mycotoxin-important fungi, dry conditions (S1) were a key driver for proliferation of Aspergillus, while Fusarium proliferation occurred irrespective of weather patterns. The relative abundance of Aspergillus and Fusarium resonated with maize aflatoxin and fumonisin-B1 levels, respectively. IMPORTANCE Fungi contaminate various crops worldwide. Maize, an important human staple and livestock cereal, is susceptible to contamination with fungi in the field. Fungi are drivers of plant disease and can compromise yield. Some species of fungi are known to produce chemical compounds (mycotoxins), which are cancer-causing agents in humans and impair livestock productivity. It is important to understand the spectrum of fungi on maize and how weather conditions can impact their abundance. This is because the abundance of fungi in the field can have a bearing on the health of the crop as well as potential for mycotoxins contamination. By understanding the spectrum of the preharvest fungi, it becomes possible to know the key fungi adapted to the maize and subsequently the potential for crop disease as well as mycotoxins contamination. The influence of weather conditions on the spectrum of preharvest fungi on maize has not been fully explored.}, }
@article {pmid37255441, year = {2023}, author = {Moen, B and Langsrud, S and Berget, I and Maugesten, T and Møretrø, T}, title = {Mapping the Kitchen Microbiota in Five European Countries Reveals a Set of Core Bacteria across Countries, Kitchen Surfaces, and Cleaning Utensils.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0026723}, doi = {10.1128/aem.00267-23}, pmid = {37255441}, issn = {1098-5336}, abstract = {The residential kitchen is often heavily colonized by microbes originating from different sources, including food and human contact. Although a few studies have reported the bacterial composition in cleaning utensils and surface samples there is limited knowledge of the bacterial diversity across different sample types, households, and countries. As part of a large European study, we have identified the microbiota of 302 samples from cleaning utensils (sponges and cloths), kitchen surfaces (sinks, cutting boards, countertops, tap handles, and a pooled sample of other handles) in 74 households across 5 countries (France, Hungary, Norway, Portugal, and Romania). In total, 31 bacterial phyla were identified, with Proteobacteria, Firmicutes, Bacteroidota, and Actinobacteria being the most abundant. Despite large variations in households with respect to kitchen standards, kitchen practices, cleaning regimes, and diet and considerable differences in bacterial diversity between samples, eight bacterial genera/families commonly associated with environmental sources were identified in most samples and defined as a core microbiota: Acinetobacter, Pseudomonas, Enhydrobacter, Enterobacteriaceae, Psychrobacter, Chryseobacterium, Bacillus, and Staphylococcus. These genera/families were also among the bacteria with the highest relative abundance across all samples, in addition to Yersiniaceae, Kocuria, Pantoea, and Streptococcus. Taxa associated with potential pathogens and fecal indicators were low in abundance but broadly distributed throughout the households. The microbial composition of surface samples indicated that the microbial composition on kitchen surfaces is more characteristic for the particular country than the object type, while the microbiota of cleaning utensils was similar across countries but differed between types (sponge or cloth). IMPORTANCE There is limited knowledge of the characteristics, differences, and similarities of the bacterial composition in residential kitchens. Here, we report the microbiota of cleaning utensils (sponges and cloths) and five different surface samples in 74 households across five European countries. In addition to increasing the knowledge of the kitchen microbiota from many geographical areas, this study identified a core microbiota in European residential kitchens despite large variations in kitchen practices and kitchen design and standards across countries and households.}, }
@article {pmid37255349, year = {2023}, author = {Cohen, SJ and Meyerovich, G and Blank, S and Ovdat, E and Loewenstein, S and Kania-Almog, J and Cohen, M and Lahat, G and Klausner, JM and Lubezky, N}, title = {Microbiota transfer following liver surgery involves microbial extracellular vesicle migration that affects liver immunity.}, journal = {Hepatology communications}, volume = {7}, number = {6}, pages = {}, doi = {10.1097/HC9.0000000000000164}, pmid = {37255349}, issn = {2471-254X}, abstract = {BACKGROUND: Short-term perioperative administration of probiotics was shown to alleviate postoperative complications and promote liver recovery among patients undergoing resection for liver malignancy. The mechanisms by which probiotic bacteria effectively influence the gut microbiome composition during the perioperative time are controversial. Here, we aim to elucidate the short-term direct biological effect of probiotic microbiota-derived vesicles on host liver cells during the perioperative period.<br><br>METHODS: Probiotic-derived vesicles (pbMVs) were administered postoperatively. pbMVs were isolated and characterized from probiotics, mainly from the bacteria genus Lactobacillus, Bifidobacterium, and Lactococcus. Mice underwent bile duct ligation, sham laparotomy (SHAM), or 70% partial hepatectomy (70%PH). pbMVs were tracked in vivo, and intrahepatic cellular and molecular aspects were analyzed by flow cytometry and qRT-PCR techniques. Liver sinusoidal endothelial cells (LSECs) analysis for Vascular Cell Adhesion Molecule-1(VCAM-1) expression following pbMV stimulation of cultured liver non-parenchymal cells which had been activated by LPS.<br><br>RESULTS: The administered pbMV rapidly translocated to the liver after surgery. pbMV administrations following surgeries enhanced neutrophil clearance; there was a dramatic decline in the liver neutrophil-to-lymphocyte ratio Ly6G+/CD3+ and an increase in IL6 levels. pbMVs reduced intrahepatic VCAM1 and ICAM2 expression compared with control following SHAM and decrease in IL10 levels following 70%PH. The administration of pbMV improved liver regeneration 72 hours following surgical liver resection with a significant decrease in IL17 expression. pbMVs modulated VCAM-1 on liver sinusoidal endothelial cells in liver cell culture.<br><br>CONCLUSIONS: Our study findings provide mechanistic insights into the liver-gut axis following surgery and illustrate how probiotic vesicles can reduce adhesion molecule expression and affect immune cell invasion and liver immunity, resulting in improved liver recovery following hepatic surgery.}, }
@article {pmid37254939, year = {2023}, author = {Gager, Y and Koppe, J and Vogl, I and Gabert, J and Jentsch, H}, title = {Antibiotic resistance genes in the subgingival microbiome and implications for periodontitis therapy.}, journal = {Journal of periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1002/JPER.22-0696}, pmid = {37254939}, issn = {1943-3670}, abstract = {UNLABELLED: Antibiotic resistance genes are widespread in periodontal pockets and are likely to affect negatively the success of antibiotic therapy.<br><br>BACKGROUND: Antibiotic resistance is emerging as a global public threat. However, it remains poorly investigated in the context of periodontal therapy. The aim of the study was to investigate the complete diversity of antibiotic resistance genes in a German population.<br><br>METHODS: Thirty-nine volunteers with periodontitis contributed to the present study with one to four periodontal pockets for a total of 124 subgingival samples. Samples were analysed using shotgun metagenomics.<br><br>RESULTS: A total of 19 antibiotic resistance genes from six antibiotic classes were detected in subgingival biofilm. Two-thirds of the volunteers (n = 26/39) showed antibiotic resistance genes for at least one of the antibiotic classes used for periodontal treatment in dental practice or research: beta-lactam, lincosamide, macrolide, nitroimidazole and tetracycline. Macrolide was the most abundant class detected (21/39 patients).<br><br>CONCLUSION(S): Findings from our study suggest a high prevalence of antibiotic resistance genes in periodontal pockets from German volunteers. We recommend the development and broader use of molecular diagnostic tests for antibiotic resistance in dental practice to ensure treatment success and minimise antibiotic resistance. This article is protected by copyright. All rights reserved.}, }
@article {pmid37254809, year = {2023}, author = {Chapuis, MP and Benoit, L and Galan, M}, title = {Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13812}, pmid = {37254809}, issn = {1755-0998}, abstract = {Gaining meaningful insights into bacterial communities associated with animal hosts requires the provision of high-quality nucleic acids. Although many studies have compared DNA extraction methods for samples with low bacterial biomass (e.g. water) or specific PCR inhibitors (e.g. plants), DNA extraction bias in samples without inherent technical constraint (e.g. animal samples) has received little attention. Furthermore, there is an urgent need to identify a DNA extraction methods in a high-throughput format that decreases the cost and time for processing large numbers of samples. We here evaluated five DNA extraction protocols, using silica membrane-based spin columns and a 96-well microplate format and based on either mechanical or enzymatic lysis or a combination of both, using three bacterial mock communities and Illumina sequencing of the V4 region of the 16SrRNA gene. Our results showed that none of the DNA extraction methods fully eliminated bias associated with unequal lysis efficiencies. However, we identified a DNA extraction method with a lower bias for each mock community standard. Of these methods, those including an enzymatic lysis showed biases specific to some bacteria. Altogether, these results again demonstrate the importance of DNA extraction standardization to be able to compare the microbiome results of different samples. In this attempt, we advise for the use of the 96-well DNeasy Blood and Tissue kit (Qiagen) with a zirconia bead-beating procedure, which optimizes altogether the cost, handling time and bacteria-specific effects associated with enzymatic lysis.}, }
@article {pmid37254732, year = {2023}, author = {Chittimalli, K and Jahan, J and Sakamuri, A and McAdams, ZL and Ericsson, AC and Jarajapu, YPR}, title = {Restoration of the gut barrier integrity and restructuring of the gut microbiome in aging by Angiotensin-(1-7).}, journal = {Clinical science (London, England : 1979)}, volume = {}, number = {}, pages = {}, doi = {10.1042/CS20220904}, pmid = {37254732}, issn = {1470-8736}, abstract = {Compromised barrier function of colon epithelium with aging is largely due to gut microbial dysbiosis. Recent studies implicate an important role for angiotensin converting enzymes, ACE and ACE2, angiotensins, and the receptors, AT1 receptor (AT1R) and Mas receptor (MasR), in the regulation of colon functions. This study tested the hypothesis that leaky gut in aging is associated with an imbalance in ACE2/ACE and that Angiotenisn-(1-7) (Ang-(1-7)) will restore epithelial barrier integrity and microbiome. Studies were carried out in Young (3-4 months) and Old (20-24 months) male mice. Ang-(1-7) was administered by using osmotic pumps. Outcome measures included expressions of ACE, ACE2, AT1R, and MasR, intestinal permeability by using FITC-dextran, and immunohistochemistry of claudin 1 and occludin, and intestinal stem cells (ISCs). ACE2 protein and activity were decreased in Old group while that of ACE were unchanged. Increased intestinal permeability and plasma levels of zonulin-1 in the Old group were normalized by Ang-(1-7). Epithelial disintegrity, number of goblet cells and ISCs in the Old group were restored by Ang-(1-7). Expression of claudin 1 and occludin in the aging colon was increased by Ang-(1-7). Infiltration of CD11b+ or F4/80+ inflammatory cells in the Old colons were decreased by Ang-(1-7). Gut microbial dysbiosis in aging was evident by decreased richness and altered beta diversity that were reversed by Ang-(1-7) with increased abundance of Lactobacillus or Lachnospiraceae. This study shows that Ang-(1-7) restores gut barrier integrity and reduces inflammation in the aging colon by restoring the ISC layer and by restructuring the gut microbiome.}, }
@article {pmid37254378, year = {2023}, author = {Park, J and Bae, D and Kim, SA}, title = {Microbial trace investigation throughout the entire chicken supply chain based on metagenomic high-throughput sequencing.}, journal = {Food research international (Ottawa, Ont.)}, volume = {169}, number = {}, pages = {112775}, doi = {10.1016/j.foodres.2023.112775}, pmid = {37254378}, issn = {1873-7145}, abstract = {As poultry possesses a high risk of contamination by various pathogens and has repeatedly been linked to foodborne outbreaks, ensuring microbiological safety throughout the chicken production chain is essential. In this study, bacterial communities in chickens and associated environments (n = 72), including feces, floors, gloves, and worktables, were trace investigated from the broiler farm, slaughterhouse, meat processing plant, and the market by amplicon sequencing of the V4 region of the 16S rRNA. The bacterial composition in live chickens along the production chain significantly changed across the stages, with distinct microbiota noted at each step. Pseudomonas, Shewanella, Acinetobacter, and Psychrobacter were dominant in the final products. Staphylococcus was abundant in live birds originally (36.83 %) but dramatically decreased after slaughter (3.07 %, 0.06 %, and 0.42 % in slaughtered, processed, and market carcasses, respectively), which may be attributed to defeathering. The proportion of Enterobacteriaceae, Acinetobacter, and Pseudomonas increased from 0.95 %, 0.03 %, and 0.04 % before slaughter to 13.57 %, 34.19 %, and 21.90 %, respectively, after slaughter, highlighting the importance of hygiene management in the succeeding steps. Diversity analysis revealed the possibility of bacterial transmission between samples from the processing plant and the market. Source tracking was performed to identify microbial contamination routes in the chicken microbiome; the major bacterial sources in the final products were the samples from the processing plant (such as processed carcasses, gloves, and worktables), accounting for 93.53 % of the total microbial sources. These results suggest that in-depth knowledge of microbial transmission between chickens and their surroundings can facilitate a precise understanding of microbiological concerns across the poultry production system and help establish safety management measures for the poultry industry.}, }
@article {pmid37254222, year = {2023}, author = {Addison, S and Armstrong, C and Wigley, K and Hartley, R and Wakelin, S}, title = {What matters most? Assessment of within-canopy factors influencing the needle microbiome of the model conifer, Pinus radiata.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {45}, pmid = {37254222}, issn = {2524-6372}, abstract = {The assembly and function of the phyllosphere microbiome is important to the overall fitness of plants and, thereby, the ecosystems they inhabit. Presently, model systems for tree phyllosphere microbiome studies are lacking, yet forests resilient to pests, diseases, and climate change are important to support a myriad of ecosystem services impacting from local to global levels. In this study, we extend the development of model microbiome systems for trees species, particularly coniferous gymnosperms, by undertaking a structured approach assessing the phyllosphere microbiome of Pinus radiata. Canopy sampling height was the single most important factor influencing both alpha- and beta-diversity of bacterial and fungal communities (p < 0.005). Bacterial and fungal phyllosphere microbiome richness was lowest in samples from the top of the canopy, subsequently increasing in the middle and then bottom canopy samples. These differences maybe driven by either by (1) exchange of microbiomes with the forest floor and soil with the lower foliage, (2) strong ecological filtering in the upper canopy via environmental exposure (e.g., UV), (3) canopy density, (4) or combinations of factors. Most taxa present in the top canopy were also present lower in tree; as such, sampling strategies focussing on lower canopy sampling should provide good overall phyllosphere microbiome coverage for the tree. The dominant phyllosphere bacteria were Alpha-proteobacteria (Rhizobiales and Sphingomonas) along with Acidobacteria Gp1. However, the P. radiata phyllosphere microbiome samples were fungal dominated. From the top canopy samples, Arthoniomycetes and Dothideomycetes were highly represented, with abundances of Arthoniomycetes then reducing in lower canopy samples whilst abundances of Ascomycota increased. The most abundant fungal taxa were Phaeococcomyces (14.4% of total reads) and Phaeotheca spp. (10.38%). A second-order effect of canopy sampling direction was evident in bacterial community composition (p = 0.01); these directional influences were not evident for fungal communities. However, sterilisation of needles did impact fungal community composition (p = 0.025), indicating potential for community differences in the endosphere versus leaf surface compartments. Needle age was only important in relation to bacterial communities, but was canopy height dependant (interaction p = 0.008). By building an understanding of the primary and secondary factors related to intra-canopy phyllosphere microbiome variation, we provide a sampling framework to either explicitly minimise or capture variation in needle collection to enable ongoing ecological studies targeted at inter-canopy or other experimental levels.}, }
@article {pmid37254173, year = {2023}, author = {Shi, M and Song, C and Xie, L and Zhang, G and Wei, Z}, title = {Role in aromatic metabolites biodegradation and adverse implication of denitrifying microbiota in kitchen waste composting.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {44}, pmid = {37254173}, issn = {2524-6372}, abstract = {BACKGROUND: Understanding the functional diversity, composition, and dynamics of microbiome is critical for quality in composting. Denitrifying microbiota, possessing multiple metabolic pathways simultaneously. Denitrification-based biodegradation of aromatic metabolites has been widely applied in the bioremediation of sediments. However, role in biodegradation of denitrifying microbiota in kitchen waste composting remain unclear. In this study, microbiome and metabolome were used to comprehensively decipher the relationship of denitrifying microbiota and aromatic metabolites, and its implication in kitchen waste (KW) composting.<br><br>RESULTS: This study was investigated by adjusting moisture content 60% as control test (CK), 70% as denitrification test (DE). In addition, one tests referred as DE&#x2009;+&#x2009;C, which received 10% of biochar to amend denitrification. Results indicated the quantities of denitrification genes narG were 1.22&#x2009;&#xd7;&#x2009;10[8] copies/g in DE at the 55th day, which were significantly higher than that in CK and DE&#x2009;+&#x2009;C (P&#x2009;<&#x2009;0.05). Similarly, the abundance of nirK gene also significantly increased in DE (P&#x2009;<&#x2009;0.05). The relative abundance of denitrification-related microbes in DE was higher than that in CK, DE&#x2009;+&#x2009;C could weaken their abundance. Metabolomics results demonstrated that metabolites were downgraded in aromatic amino acid and catechin metabolic pathways in DE, which were identified as precursors to synthesis key product fulvic acid. The concentrations of fulvic acid dramatically decreased 21.05&#xa0;mg/g in DE comparison with CK. Biochar addition alleviated the biodegradation of aromatic metabolites and reduced the utilization of fulvic acid. Integrative analyses of metabolomics and microbiome suggested that the microbiota involved in nitrite reduction pathway was vital for the biodegradation aromatic metabolites. Mantel test verified that NO3[-]-N, moisture content, eta, environmental factors were important drivers behind the changes in the denitrifying microbiota biodegradation function.<br><br>CONCLUSION: The data confirm the biodegradation function of denitrifying microbiota led to the loss of core product fulvic acid in KW composting, which highlighted the adverse role and implication of denitrification for composting humification. Control of denitrification with biochar was recommended to improve composting quality.}, }
@article {pmid37254162, year = {2023}, author = {Zhu, X and Shen, J and Feng, S and Huang, C and Wang, H and Huo, F and Liu, H}, title = {Akkermansia muciniphila, which is enriched in the gut microbiota by metformin, improves cognitive function in aged mice by reducing the proinflammatory cytokine interleukin-6.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {120}, pmid = {37254162}, issn = {2049-2618}, abstract = {BACKGROUND: Metformin, a type 2 diabetes treatment, improves the cognitive function of aged mice; however, whether the protective effects of metformin on cognitive function in aged mice are associated with the gut microbiome is poorly understood. Although some studies suggest that the gut microbe composition influences cognitive function and that manipulating the gut microbiota might protect against age-related cognitive dysfunction, there is no direct evidence to validate that the gut microbiota mediates the effect of metformin on cognitive improvement.<br><br>RESULTS: In this study, we show that the gut microbiota is altered by metformin, which is necessary for protection against ageing-associated cognitive function declines in aged mice. Mice treated with antibiotics did not exhibit metformin-mediated cognitive function protection. Moreover, treatment with Akkermansia muciniphila, which is enriched by metformin, improved cognitive function in aged mice. Mechanistically, A. muciniphila decreased pro-inflammatory-associated pathways, particularly that of the pro-inflammatory cytokine interleukin (IL)-6, in both the peripheral blood and hippocampal profiles, which was correlated with cognitive function improvement. An IL-6 antibody protected cognitive function, and an IL-6 recombinant protein abolished the protective effect of A. muciniphila on cognitive function in aged mice.<br><br>CONCLUSION: This study reveals that A. muciniphila, which is mediated in the gut microbiota by metformin, modulates inflammation-related pathways in the host and improves cognitive function in aged mice by reducing the pro-inflammatory cytokine IL-6. Video Abstract.}, }
@article {pmid37254152, year = {2023}, author = {Wang, K and Mehta, RS and Ma, W and Nguyen, LH and Wang, DD and Ghazi, AR and Yan, Y and Al-Shaar, L and Wang, Y and Hang, D and Fu, BC and Ogino, S and Rimm, EB and Hu, FB and Carmody, RN and Garrett, WS and Sun, Q and Chan, AT and Huttenhower, C and Song, M}, title = {The gut microbiome modifies the associations of short- and long-term physical activity with body weight changes.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {121}, pmid = {37254152}, issn = {2049-2618}, support = {R35 CA197735/NH/NIH HHS/United States ; K24 DK098311/NH/NIH HHS/United States ; R00 CA215314/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: The gut microbiome regulates host energy balance and adiposity-related metabolic consequences, but it remains unknown how the gut microbiome modulates body weight response to physical activity (PA).<br><br>METHODS: Nested in the Health Professionals Follow-up Study, a subcohort of 307 healthy men (mean[SD] age, 70[4] years) provided stool and blood samples in 2012-2013. Data from cohort long-term follow-ups and from the accelerometer, doubly labeled water, and plasma biomarker measurements during the time of stool collection were used to assess long-term and short-term associations of PA with adiposity. The gut microbiome was profiled by shotgun metagenomics and metatranscriptomics. A subcohort of 209 healthy women from the Nurses' Health Study II was used for validation.<br><br>RESULTS: The microbial species Alistipes putredinis was found to modify the association between PA and body weight. Specifically, in individuals with higher abundance of A. putredinis, each 15-MET-hour/week increment in long-term PA was associated with 2.26&#xa0;kg (95% CI, 1.53-2.98&#xa0;kg) less weight gain from age 21 to the time of stool collection, whereas those with lower abundance of A. putredinis only had 1.01&#xa0;kg (95% CI, 0.41-1.61&#xa0;kg) less weight gain (pinteraction&#x2009;=&#x2009;0.019). Consistent modification associated with A. putredinis was observed for short-term PA in relation to BMI, fat mass%, plasma HbA1c, and 6-month weight change. This modification effect might be partly attributable to four metabolic pathways encoded by A. putredinis, including folate transformation, fatty acid &#x3b2;-oxidation, gluconeogenesis, and stearate biosynthesis.<br><br>CONCLUSIONS: A greater abundance of A. putredinis may strengthen the beneficial association of PA with body weight change, suggesting the potential of gut microbial intervention to improve the efficacy of PA in body weight management. Video Abstract.}, }
@article {pmid37253538, year = {2023}, author = {Mori, H and Kato, T and Ozawa, H and Sakamoto, M and Murakami, T and Taylor, TD and Toyoda, A and Ohkuma, M and Kurokawa, K and Ohno, H}, title = {Assessment of metagenomic workflows using a newly constructed human gut microbiome mock community.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {30}, number = {3}, pages = {}, doi = {10.1093/dnares/dsad010}, pmid = {37253538}, issn = {1756-1663}, abstract = {To quantify the biases introduced during human gut microbiome studies, analyzing an artificial mock community as the reference microbiome is indispensable. However, there are still limited resources for a mock community which well represents the human gut microbiome. Here, we constructed a novel mock community comprising the type strains of 18 major bacterial species in the human gut and assessed the influence of experimental and bioinformatics procedures on the 16S rRNA gene and shotgun metagenomic sequencing. We found that DNA extraction methods greatly affected the DNA yields and taxonomic composition of sequenced reads, and that some of the commonly used primers for 16S rRNA genes were prone to underestimate the abundance of some gut commensal taxa such as Erysipelotrichia, Verrucomicrobiota and Methanobacteriota. Binning of the assembled contigs of shotgun metagenomic sequences by MetaBAT2 produced phylogenetically consistent, less-contaminated bins with varied completeness. The ensemble approach of multiple binning tools by MetaWRAP can improve completeness but sometimes increases the contamination rate. Our benchmark study provides an important foundation for the interpretation of human gut microbiome data by providing means for standardization among gut microbiome data obtained with different methodologies and will facilitate further development of analytical methods.}, }
@article {pmid37253485, year = {2023}, author = {Chen, L and Guo, L and Feng, S and Wang, C and Cui, Z and Wang, S and Lu, Q and Chang, H and Hang, B and Snijders, AM and Mao, JH and Lu, Y and Ding, D}, title = {Fecal microbiota transplantation ameliorates type 2 diabetes via metabolic remodeling of the gut microbiota in db/db mice.}, journal = {BMJ open diabetes research &amp; care}, volume = {11}, number = {3}, pages = {}, doi = {10.1136/bmjdrc-2022-003282}, pmid = {37253485}, issn = {2052-4897}, abstract = {INTRODUCTION: Gut microbiome (GM) deregulation has been implicated in major conditions such as obesity and type 2 diabetes (T2DM). Our previous prospective study indicated that fecal microbiota transplantation (FMT) successfully improved patients with T2DM. We hypothesized that FMT may be a potential therapeutic method for T2DM, but its precise mechanisms in T2DM remains to be elucidated.<br><br>RESEARCH DESIGN AND METHODS: Eight db/m mice were FMT donors and control mice, and 16 genetically diabetic db/db mice were equally divided into two groups (db/db+phosphate-buffered saline (PBS) group, db/db+FMT group). The db/db+FMT group was administered fresh fecal suspension (0.2 mL/mice) daily for 4&#x2009;weeks. Analysis of the GM and serum metabolome was carried out by 16S ribosomal RNA sequencing and liquid chromatogram-mass spectrometry, respectively. Effects of FMT on the gut barrier and pancreas were assessed using protein assays, messenger RNA, immunohistology and clinical indicators testing.<br><br>RESULTS: Our results showed that FMT treatment of db/db mice relieves a series of clinical indicators, including fasting plasma glucose, serum insulin and oral glucose tolerance test among others. Compared with non-diabetic control mice, db/db+PBS mice exhibited decreased abundance of Ruminococaceae, Porphyromonadaceae and increased abundance of Rikenellaceae and Lactobacillaceae. FMT treatment reversed this effect on the microbiome. Eleven metabolites were changed between the db/db+PBS&#x2009;and db/db+FMT groups. Correlation analysis showed that the structural changes of the GM were correlated with host metabolite levels. We further showed that FMT treatment of db/db mice improved intestinal barrier function, reduced inflammation and caused an alteration in the number of circulating immune cells.<br><br>CONCLUSIONS: FMT-mediated changes in the GM, serum metabolites, intestinal epithelial barrier, inflammation and circulating immune cells play an important role in the efficacy of FMT on T2DM disease progression.}, }
@article {pmid37253482, year = {2023}, author = {Paton, SEJ and Solano, JL and Coulombe-Rozon, F and Lebel, M and Menard, C}, title = {Barrier-environment interactions along the gut-brain axis and their influence on cognition and behaviour throughout the lifespan.}, journal = {Journal of psychiatry &amp; neuroscience : JPN}, volume = {48}, number = {3}, pages = {E190-E208}, doi = {10.1503/jpn.220218}, pmid = {37253482}, issn = {1488-2434}, abstract = {Environment is known to substantially alter mental state and behaviour across the lifespan. Biological barriers such as the blood-brain barrier (BBB) and gut barrier (GB) are major hubs for communication of environmental information. Alterations in the structural, social and motor environment at different stages of life can influence function of the BBB and GB and their integrity to exert behavioural consequences. Importantly, each of these environmental components is associated with a distinct immune profile, glucocorticoid response and gut microbiome composition, creating unique effects on the BBB and GB. These barrier-environment interactions are sensitive to change throughout life, and positive or negative alterations at critical stages of development can exert long-lasting cognitive and behavioural consequences. Furthermore, because loss of barrier integrity is implicated in pathogenesis of mental disorders, the pathways of environmental influence represent important areas for understanding these diseases. Positive environments can be protective against stress- and age-related damage, raising the possibility of novel pharmacological targets. This review summarizes known mechanisms of environmental influence - such as social interactions, structural complexity and physical exercise - on barrier composition, morphology and development, and considers the outcomes and implications of these interactions in the context of psychiatric disorders.}, }
@article {pmid37253106, year = {2023}, author = {Sato, T and Sato, S}, title = {Circadian Regulation of Metabolism - Commitment to Health and Diseases.}, journal = {Endocrinology}, volume = {}, number = {}, pages = {}, doi = {10.1210/endocr/bqad086}, pmid = {37253106}, issn = {1945-7170}, abstract = {The circadian clock is a biological time-keeping system to govern temporal rhythms of the endocrine system and metabolism. The master pacemaker of biological rhythms is housed in the hypothalamic suprachiasmatic nucleus (SCN) where approximately 20,000 neurons exist and receive light stimulus as a predominant timed external cue (zeitgeber). The central SCN clock orchestrates molecular clock rhythms in peripheral tissues and coordinates circadian metabolic homeostasis at a systemic level. Accumulated evidence underscores an intertwined relationship between the circadian clock system and metabolism: the circadian clock provides daily dynamics of metabolic activity whereas the circadian clock activity is modulated by metabolic and epigenetic mechanisms. Disruption of circadian rhythms due to shift work and jet lag confounds the daily metabolic cycle, thereby increasing risks of various metabolic diseases, such as obesity and type 2 diabetes (T2D). Food intake serves as a powerful zeitgeber to entrain molecular clocks and circadian clock regulation of metabolic pathways, independently of light exposure to the SCN. Thus, the daily timing of food intake rather than the diet quantity and quality contributes to promoting health and preventing disease development through restoring circadian control of metabolic pathways. In this review, we discuss how the circadian clock dominates metabolic homeostasis and how chrono-nutritional strategies benefit metabolic health, summarizing the latest evidence from basic and translational studies.}, }
@article {pmid37253061, year = {2023}, author = {Van Doren, VE and Smith, SA and Hu, YJ and Tharp, G and Bosinger, S and Ackerley, CG and Murray, PM and Amara, RR and Amancha, PK and Arthur, RA and Johnston, HR and Kelley, CF}, title = {HIV, asymptomatic STI, and the rectal mucosal immune environment among young men who have sex with men.}, journal = {PLoS pathogens}, volume = {19}, number = {5}, pages = {e1011219}, doi = {10.1371/journal.ppat.1011219}, pmid = {37253061}, issn = {1553-7374}, abstract = {Young men who have sex with men (YMSM) are disproportionately affected by HIV and bacterial sexually transmitted infections (STI) including gonorrhea, chlamydia, and syphilis; yet research into the immunologic effects of these infections is typically pursued in siloes. Here, we employed a syndemic approach to understand potential interactions of these infections on the rectal mucosal immune environment among YMSM. We enrolled YMSM aged 18-29 years with and without HIV and/or asymptomatic bacterial STI and collected blood, rectal secretions, and rectal tissue biopsies. YMSM with HIV were on suppressive antiretroviral therapy (ART) with preserved blood CD4 cell counts. We defined 7 innate and 19 adaptive immune cell subsets by flow cytometry, the rectal mucosal transcriptome by RNAseq, and the rectal mucosal microbiome by 16S rRNA sequencing and examined the effects of HIV and STI and their interactions. We measured tissue HIV RNA viral loads among YMSM with HIV and HIV replication in rectal explant challenge experiments among YMSM without HIV. HIV, but not asymptomatic STI, was associated with profound alterations in the cellular composition of the rectal mucosa. We did not detect a difference in the microbiome composition associated with HIV, but asymptomatic bacterial STI was associated with a higher probability of presence of potentially pathogenic taxa. When examining the rectal mucosal transcriptome, there was evidence of statistical interaction; asymptomatic bacterial STI was associated with upregulation of numerous inflammatory genes and enrichment for immune response pathways among YMSM with HIV, but not YMSM without HIV. Asymptomatic bacterial STI was not associated with differences in tissue HIV RNA viral loads or in HIV replication in explant challenge experiments. Our results suggest that asymptomatic bacterial STI may contribute to inflammation particularly among YMSM with HIV, and that future research should examine potential harms and interventions to reduce the health impact of these syndemic infections.}, }
@article {pmid37252860, year = {2023}, author = {Du, G and Jiang, X and Han, X and Pan, L and Tang, G}, title = {Preliminary analysis of the buccal mucosal fungal microbiome in oral lichen planus patients.}, journal = {Journal of oral pathology &amp; medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jop.13439}, pmid = {37252860}, issn = {1600-0714}, abstract = {OBJECTIVE: To determine the structure and co-occurrence patterns of mucosal fungal community in oral lichen planus (OLP) patients.<br><br>SUBJECTS AND METHODS: Mucosal swab samples from 20 OLP patients and 10 healthy controls (HCs) were collected and the mucosal mycobiomes were sequenced. The abundance, frequency, and diversity of fungi were analyzed, as well as the inter-genera interactions. The associations between fungal genera and OLP severity were further identified.<br><br>RESULTS: At the genus level, the relative abundance of unclassified_Trichocomaceae was significantly decreased in the reticular and erosive OLP groups compared to HCs. Meanwhile, significantly lower levels of Pseudozyma were observed in the reticular OLP group compared to HCs. The negative:positive cohesiveness ratio was significantly lower in the OLP group than HCs, indicating a relatively unstable fungal ecological system in the OLP group. In the OLP group, the abundance of unclassified_Nectriaceae was significantly correlated with the reticulation/erythema/ulceration (REU) score.<br><br>CONCLUSIONS: Compared to HCs, the decreased stability of fungal communities and the decreased abundances of two genera (unclassified_Trichocomaceae and Pseudozyma) on buccal mucosa were identified in OLP patients.}, }
@article {pmid37150398, year = {2023}, author = {Chan, KW and Hebert, J and Radford-Smith, D and Anthony, DC and Burnet, PWJ}, title = {Live or heat-killed probiotic administration reduces anxiety and central cytokine expression in BALB/c mice, but differentially alters brain neurotransmitter gene expression.}, journal = {Neuropharmacology}, volume = {235}, number = {}, pages = {109565}, doi = {10.1016/j.neuropharm.2023.109565}, pmid = {37150398}, issn = {1873-7064}, abstract = {While the potential for probiotic supplements to act as adjunctive treatments for mood disorders has been widely demonstrated, the precise mode of action remains unclear. To investigate the psychotropic effects of a multi-species probiotic on emotional behaviour in male BALB/c mice, we explored the potential mechanisms of action relating to the temporal changes in the mRNA expression of brain cytokines, BDNF, central 5HT receptor and serotonin transporter (SERT) and GABA receptor in the context of probiotic induced behavioural changes. The effects of a heat-killed probiotic, independent of microbial metabolic processes were also evaluated on the same outcomes to understand whether the host response to the bacteria is more or less important than the contribution of the metabolic activity of the bacteria themselves. Results showed that probiotic supplementation reduced anxiety-like behaviours, increased time spent in the light area of the light-dark box, and decreased the expression of pro-inflammatory cytokines in the brain. Furthermore, probiotic administration elevated hippocampal BDNF and decreased GABAB1β expression. Interestingly, the heat-killed probiotic and its membrane fraction had similar effects on emotional behaviours and gene expression in the brain. The ingestion of live and heat-killed probiotic preparations also reduced TLR2 expression in the gut. Thus, the present study reveals that the anxiolytic action of a multispecies probiotic in BALB/c mice is independent of bacterial viability. This suggests that it is the host response to probiotics, rather than microbial metabolism that facilitates the molecular changes in the brain and downstream behaviours. This article is part of the Special Issue on "Microbiome &amp; the Brain: Mechanisms &amp; Maladies".}, }
@article {pmid37252000, year = {2023}, author = {Gu, JD and Katayama, Y}, title = {Bats, monkeys and plants in the time of Covid-19 pandemic at Angkor monuments.}, journal = {International biodeterioration &amp; biodegradation}, volume = {182}, number = {}, pages = {105623}, pmid = {37252000}, issn = {0964-8305}, abstract = {Knowledge of biodeterioration and protection of cultural heritage depends on the scientific understanding of the substratum materials, the ambient environment, the fauna and flora including the microorganisms so an overall picture can be constructed to serve as a basis for protection and management. Over the past more than 20 years of survey and research, an accumulated dataset is available on the mechanisms on the (bio)deterioration of stone monuments in Cambodia, involving interactions among water cycling and salt dynamics with the presence of a rich surface microbiome, the biofilms. However, during the Covid-19 period (2020-2022), because of a drastic drop on tourist population, the number of bats and monkeys are on the rising, which have an impact on the on-going protection efforts. At the same time, large trees around and on the cultural heritage sites are being managed by trimming and removal to decrease the potential risk and negative impacts from them. The new management scheme needs scientific results for the long-term successful protection of these cultural heritage. A close examination of these issues is also meaningful and important to the research new initiatives and policy to be implemented not only in Cambodia but also elsewhere.}, }
@article {pmid37251966, year = {2023}, author = {Takagi, T and Kunihiro, T and Takahashi, S and Hisada, T and Nagashima, K and Mochizuki, J and Mizushima, K and Naito, Y}, title = {A newly developed solution for the preservation of short-chain fatty acids, bile acids, and microbiota in fecal specimens.}, journal = {Journal of clinical biochemistry and nutrition}, volume = {72}, number = {3}, pages = {263-269}, pmid = {37251966}, issn = {0912-0009}, abstract = {Recent studies have revealed that the gut microbiome affects various health conditions via its metabolites, including short-chain fatty acids (SCFAs) and bile acids (BAs). In the analysis of these, appropriate collection, handling, and storage of fecal specimens are required, and convenient specimen handling processes will facilitate their investigation. Here, we developed a novel preservation solution, "Metabolokeeper[®]", to stabilize fecal microbiota, organic acids including SCFAs, and BAs at room temperature. In the present study, we collected fecal samples from 20 healthy adult volunteers and stored them at room temperature with Metabolokeeper[®] and at -80°C without preservatives for up to four weeks to evaluate the usefulness of the novel preservative solution. We found that microbiome profiles and short chain fatty acid contents were stably maintained at room temperature with Metabolokeeper[®] for 28 days, while the bile acids were stably maintained for 7 days under the same conditions. We conclude that this convenient procedure to obtain a fecal sample for collecting the gut microbiome and gut metabolites can contribute to a better understanding of the health effects of fecal metabolites produced by the gut microbiome.}, }
@article {pmid37251444, year = {2023}, author = {Tian, T and Zhou, Y and Xu, Y and Xu, Y}, title = {Intestinal microbial 16S sequencing and LC-MS metabonomic analysis revealed differences between young and old cats.}, journal = {Heliyon}, volume = {9}, number = {6}, pages = {e16417}, pmid = {37251444}, issn = {2405-8440}, abstract = {With the progress of society, the health problems of pets have attracted more and more attention. Recent studies have shown that intestinal microflora and related fecal metabolites play a crucial role in the healthy growth of cats. However, the potential role and related metabolic characteristics of gut microbiota in different age groups of pet cats need to be further clarified. 16S rRNA gene sequencing was used to analyze the intestinal microbial composition of young and old cats. LC-MS metabonomic analysis is used to characterize the changes in the metabolic spectrum in feces. The potential relationship between intestinal microorganisms and metabolites, as well as the differences in different age groups, were studied. The species composition of intestinal microflora in the young group and old group is significantly different, T-test algorithm shows 36 different ASVs and 8 different genuses, while the Wilcoxon algorithm shows 81 different ASVs and 17 different genuses. The metabolomics analysis identified 537 kinds of fecal metabolites, which are rich in differences between young and old cats, and may be potential biomarkers indicating the health of cats. 16S rRNA analysis showed significant differences in fructose and mannose metabolism, while metabonomics KEGG analysis showed significant difference in choline metabolism in cancer. Our study compared the differences between the intestinal microbiome and fecal metabolites in young and old cats. This difference provides a new direction for further exploring the relationship between the composition and metabolism of intestinal microbiota in cats of different age groups. It also provides a reference for cat health research.}, }
@article {pmid37251382, year = {2023}, author = {Bleich, D}, title = {Editorial: 21st century advances in type 1 diabetes research and immunotherapy.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1213417}, doi = {10.3389/fimmu.2023.1213417}, pmid = {37251382}, issn = {1664-3224}, }
@article {pmid37251147, year = {2023}, author = {Nurxat, N and Wang, L and Wang, Q and Li, S and Jin, C and Shi, Y and Wulamu, A and Zhao, N and Wang, Y and Wang, H and Li, M and Liu, Q}, title = {Commensal Staphylococcus epidermidis Defends against Staphylococcus aureus through SaeRS Two-Component System.}, journal = {ACS omega}, volume = {8}, number = {20}, pages = {17712-17718}, pmid = {37251147}, issn = {2470-1343}, abstract = {Staphylococcus aureus is a high-virulent Gram-positive pathogen that is responsible for a serious of diseases. The emergence of antibiotic-resistant S. aureus poses a significant challenge in terms of treatment. The recent research on the human microbiome suggested that the application of commensal bacteria is a new strategy for combating pathogenic infections. Staphylococcus epidermidis, one of the most abundant species in the nasal microbiome, is able to inhibit the colonization of S. aureus. However, during bacterial competition, S. aureus undergoes evolutionary changes to adapt to the diverse environment. Our study has demonstrated that the nasal colonized S. epidermidis possesses the ability to inhibit the hemolytic activity of S. aureus. Moreover, we deciphered another layer of mechanism to inhibit S. aureus colonization by S. epidermidis. The active component present in the cell-free culture of S. epidermidis was found to significantly reduce the hemolytic activity of S. aureus in SaeRS- and Agr-dependent manner. Specifically, the hemolytic inhibition on the S. aureus Agr-I type by S. epidermidis is primarily dependent on the SaeRS two-component system. The active component is characterized as a small molecule that is heat sensitive and protease resistant. Critically, S. epidermidis significantly inhibit the virulence of S. aureus in a mouse skin abscess model, suggesting that the active compound could potentially be used as a therapeutic agent for managing S. aureus infections.}, }
@article {pmid37250794, year = {2023}, author = {Kitsios, GD and Nguyen, VD and Sayed, K and Al-Yousif, N and Schaefer, C and Shah, FA and Bain, W and Yang, H and Fitch, A and Li, K and Wang, X and Qin, S and Gentry, H and Zhang, Y and Varon, J and Arciniegas Rubio, A and Englert, JA and Baron, RM and Lee, JS and Methé, B and Benos, PV and Morris, A and McVerry, BJ}, title = {The upper and lower respiratory tract microbiome in severe aspiration pneumonia.}, journal = {iScience}, volume = {26}, number = {6}, pages = {106832}, pmid = {37250794}, issn = {2589-0042}, abstract = {Uncertainty persists whether anaerobic bacteria represent important pathogens in aspiration pneumonia. In a nested case-control study of mechanically ventilated patients classified as macro-aspiration pneumonia (MAsP, n = 56), non-macro-aspiration pneumonia (NonMAsP, n = 91), and uninfected controls (n = 11), we profiled upper (URT) and lower respiratory tract (LRT) microbiota with bacterial 16S rRNA gene sequencing, measured plasma host-response biomarkers, analyzed bacterial communities by diversity and oxygen requirements, and performed unsupervised clustering with Dirichlet Multinomial Models (DMM). MAsP and NonMAsP patients had indistinguishable microbiota profiles by alpha diversity and oxygen requirements with similar host-response profiles and 60-day survival. Unsupervised DMM clusters revealed distinct bacterial clusters in the URT and LRT, with low-diversity clusters enriched for facultative anaerobes and typical pathogens, associated with higher plasma levels of SPD and sCD14 and worse 60-day survival. The predictive inter-patient variability in these bacterial profiles highlights the importance of microbiome study in patient sub-phenotyping and precision medicine approaches for severe pneumonia.}, }
@article {pmid37250704, year = {2023}, author = {Chen, S and Cao, P and Li, T and Wang, Y and Liu, X}, title = {Microbial diversity patterns in the root zone of two Meconopsis plants on the Qinghai-Tibet Plateau.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15361}, pmid = {37250704}, issn = {2167-8359}, abstract = {In the extreme alpine climate of the Qinghai-Tibet Plateau (QTP), plant growth and reproduction are limited by extremely cold temperatures, low soil moisture, and scarce nutrient availability. The root-associated microbiome indirectly promotes plant growth and plays a role in the fitness of plants on the QTP, particularly in Tibetan medicinal plants. Despite the importance of the root-associated microbiome, little is known about the root zone. This study used high-throughput sequencing to investigate two medicinal Meconopsis plants, M. horridula and M. integrifolia, to determine whether habitat or plant identity had a more significant impact on the microbial composition of the roots. The fungal sequences were obtained using ITS-1 and ITS-2, and bacterial sequences were obtained using 16S rRNA. Different microbial patterns were observed in the microbial compositions of fungi and bacteria in the root zones of two Meconopsis plants. In contrast to bacteria, which were not significantly impacted by plant identity or habitat, the fungi in the root zone were significantly impacted by plant identity, but not habitat. In addition, the synergistic effect was more significant than the antagonistic effect in the correlation between fungi and bacteria in the root zone soil. The fungal structure was influenced by total nitrogen and pH, whereas the structure of bacterial communities was influenced by soil moisture and organic matter. Plant identity had a greater influence on fungal structure than habitat in two Meconopsis plants. The dissimilarity of fungal communities suggests that more attention should be paid to fungi-plant interactions.}, }
@article {pmid37250301, year = {2023}, author = {Gerace, E and Baldi, S and Salimova, M and Di Gloria, L and Curini, L and Cimino, V and Nannini, G and Russo, E and Pallecchi, M and Ramazzotti, M and Bartolucci, G and Occupati, B and Lanzi, C and Scarpino, M and Lanzo, G and Grippo, A and Lolli, F and Mannaioni, G and Amedei, A}, title = {Oral and fecal microbiota perturbance in cocaine users: Can rTMS-induced cocaine abstinence support eubiosis restoration?.}, journal = {iScience}, volume = {26}, number = {5}, pages = {106627}, pmid = {37250301}, issn = {2589-0042}, abstract = {The effects of cocaine on microbiota have been scarcely explored. Here, we investigated the gut (GM) and oral (OM) microbiota composition of cocaine use disorder (CUD) patients and the effects of repetitive transcranial magnetic stimulation (rTMS). 16S rRNA sequencing was used to characterize GM and OM, whereas PICRUST2 assessed functional changes in microbial communities, and gas-chromatography was used to evaluate fecal short and medium chain fatty acids. CUD patients reported a significant decrease in alpha diversity and modification of the abundances of several taxa in both GM and OM. Furthermore, many predicted metabolic pathways were differentially expressed in CUD patients' stool and saliva samples, as well as reduced levels of butyric acid that appear restored to normal amounts after rTMS treatment. In conclusion, CUD patients showed a profound dysbiotic fecal and oral microbiota composition and function and rTMS-induced cocaine abstinence determined the restoration of eubiotic microbiota.}, }
@article {pmid37250058, year = {2023}, author = {, }, title = {Retraction: Microbiome-based hypothesis on Ivermectin's mechanism in COVID-19: Ivermectin feeds bifidobacteria to boost immunity.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1216170}, doi = {10.3389/fmicb.2023.1216170}, pmid = {37250058}, issn = {1664-302X}, abstract = {[This retracts the article DOI: 10.3389/fmicb.2022.952321.].}, }
@article {pmid37250055, year = {2023}, author = {Wang, X and Wu, Y and Liu, Y and Chen, F and Chen, S and Zhang, F and Li, S and Wang, C and Gong, Y and Huang, R and Hu, M and Ning, Y and Zhao, H and Guo, X}, title = {Altered gut microbiome profile in patients with knee osteoarthritis.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1153424}, pmid = {37250055}, issn = {1664-302X}, abstract = {INTRODUCTION: Osteoarthritis (OA) is a kind of chronic, degenerative disorder with unknown causes. In this study, we aimed to improve our understanding of the gut microbiota profile in patients with knee OA.<br><br>METHODS: 16S rDNA gene sequencing was performed to detect the gut microbiota in fecal samples collected from the patients with OA (n&#x2009;=&#x2009;32) and normal control (NC, n&#x2009;=&#x2009;57). Then the metagenomic sequencing was used to identify the genes or functions linked with gut microbial changes at the species level in the fecal samples from patients with OA and NC groups.<br><br>RESULTS: The Proteobacteria was identified as dominant bacteria in OA group. We identified 81 genera resulted significantly different in abundance between OA and NC. The abundance of Agathobacter, Ruminococcus, Roseburia, Subdoligranulum, and Lactobacillus showed significant decrease in the OA compared to the NC. The abundance of genera Prevotella_7, Clostridium, Flavonifractor and Klebsiella were increasing in the OA group, and the families Lactobacillaceae, Christensenellaceae, Clostridiaceae_1 and Acidaminococcaceae were increasing in the NC. The metagenomic sequencing showed that the abundance of Bacteroides stercoris, Bacteroides vulgatus and Bacteroides uniformis at the species level were significantly decreasing in the OA, and the abundance of Escherichia coli, Klebsiella pneumoniae, Shigella flexneri and Streptococcus salivarius were significantly increased in OA.<br><br>DISCUSSION: The results of our study interpret a comprehensive profile of the gut microbiota in patients with knee OA and offer the evidence that the cartilage-gut-microbiome axis could play a crucial role in underlying the mechanisms and pathogenesis of OA.}, }
@article {pmid37250027, year = {2023}, author = {Sun, H and Xu, W and Gu, T and Sun, J and Li, C and Chen, L and Tian, Y and Li, G and Lu, L and Zeng, T}, title = {Association of residual feed intake with intestinal microbiome and metabolome in laying period of ducks.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1138914}, pmid = {37250027}, issn = {1664-302X}, abstract = {INTRODUCTION: Residual feed intake (RFI) is a indicator to evaluate animal feed. This experiment was explored to study the relationship between intestinal microbiome and metabolome of ducks with different residual feed intake during laying period.<br><br>METHODS: A total of 300 Shaoxing ducks aged 42&#x2009;weeks were randomly selected and fed a diet of 60 d. At the end of the trial, 20 samples were selected according to the phenotype of RFI and divided into two groups (HRFI and LRFI). The cecal microbiota composition was explored by 16S ribosomal RNA gene sequencing and rectal metabolomics uses liquid chromatography-mass spectrometry (LC-MS) to identify the composition of metabolites in a non-targeted manner.<br><br>RESULTS: Results show feed intake and feed conversion ratio in the group HRFI were significantly higher than those in the group LRFI (p <&#x2009;0.05). Chao1 indices were higher in the group LRFI than in the HRFI (p <&#x2009;0.05), Shannon and Simpson indices were higher in the group LRFI than in the HRFI (p <&#x2009;0.01). After linear discriminant analysis effect size (p <&#x2009;0.05, LDA score&#x2009;>&#x2009;3), Rikenellaceae, Rikenellaceae_RC9_gut_group, Lactobacillales and Ruminococcus_2, etc. were significantly enriched in the group LRFI at the genus level, while Prevotellaceae_NK3B31_group and Bacteria were significantly enriched in the group HRFI. After LC-MS analysis we found 338 metabolic difference products and 10 metabolic pathways, including the ABC transporter system, cysteine and methionine metabolism, arginine and proline metabolism, and vitamin B6 metabolism, were identified to be associated with the significantly differentially expressed between the groups LRFI and HRFI (p <&#x2009;0.05). We hypothesize that the difference between ducks with different RFIs is mainly due to the fact that ducks with LRFI have more SCFAs-producing bacteria in their gut microorganisms, which regulate the RFI of animals. This process we found that Phascolarctobaterium and Anaerobiospirillum may provide energy for ABC transporter system by producing SCFAs, and regulate RFI to improve feed utilization efficiency.<br><br>DISCUSSION: These results revealed the relationship between microbiome and metabonomics in laying ducks with different RFI, and provided theoretical basis for further study on the relationship between them.}, }
@article {pmid37250025, year = {2023}, author = {Dahal, RH and Kim, S and Kim, YK and Kim, ES and Kim, J}, title = {Insight into gut dysbiosis of patients with inflammatory bowel disease and ischemic colitis.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1174832}, pmid = {37250025}, issn = {1664-302X}, abstract = {The collection of whole microbial communities (bacteria, archaea, fungi, and viruses) together constitutes the gut microbiome. Diet, age, stress, host genetics, and diseases cause increases or decreases in the relative abundance and diversity of bacterial species (dysbiosis). We aimed to investigate the gut microbial composition at different taxonomic levels of healthy controls (HCs) with active Crohn's disease (CD), ulcerative colitis (UC), and ischemic colitis (IC) using culture- and non-culture-based approaches and identify biomarkers to discriminate CD, UC, or IC. We determined the specific changes in the gut microbial profile using culture-independent (16S rRNA gene amplicon sequencing) as well as culture-based (culturomic) approaches. Biomarkers were validated using quantitative Real-Time PCR (qPCR). In both methods, bacterial diversity and species richness decreased in disease-associated conditions compared with that in HCs. Highly reduced abundance of Faecalibacterium prausnitzii and Prevotella sp. and an increased abundance of potentially pathogenic bacteria such as Enterococcus faecium, Enterococcus faecalis, and Escherichia coli in all CD, UC, or IC conditions were observed. We noted a high abundance of Latilactobacillus sakei in CD patients; Ligilactobacillus ruminis in UC patients; and Enterococcus faecium, Escherichia coli, and Enterococcus faecalis in IC patients. Highly reduced abundance of Faecalibacterium prausnitzii in all cases, and increased abundance of Latilactobacillus sakei and Enterococcus faecium in CD, Ligilactobacillus ruminis and Enterococcus faecium in UC, and Enterococcus faecium, Escherichia coli, and Enterococcus faecalis in IC could be biomarkers for CD, UC, and IC, respectively. These biomarkers may help in IBD (CD or UC) and IC diagnosis.}, }
@article {pmid37249985, year = {2023}, author = {, }, title = {Erratum: Gut and genital tract microbiomes: dysbiosis and link to gynecological disorders.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1211349}, doi = {10.3389/fcimb.2023.1211349}, pmid = {37249985}, issn = {2235-2988}, abstract = {[This corrects the article DOI: 10.3389/fcimb.2022.1059825.].}, }
@article {pmid37249979, year = {2023}, author = {Chen, C and Chen, K and Huang, Z and Huang, X and Wang, Z and He, F and Qin, M and Long, C and Tang, B and Mo, X and Liu, J and Tang, W}, title = {Identification of intestinal microbiome associated with lymph-vascular invasion in colorectal cancer patients and predictive label construction.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1098310}, pmid = {37249979}, issn = {2235-2988}, abstract = {OBJECTIVE: To identify differences between the composition, abundance, and biological function of the intestinal microbiome of patients with and without lymph-vascular invasion (LVI) colorectal cancer (CRC) and to construct predictive labels to support accurate assessment of LVI in CRC.<br><br>METHOD: 134 CRC patients were included, which were divided into two groups according to the presence or absence of LVI, and their intestinal microbiomes were sequenced by 16SrRNA and analyzed for differences. The transcriptome sequencing data of 9 CRC patients were transformed into immune cells abundance matrix by CIBERSORT algorithm, and the correlation among LVI-associated differential intestinal microbiomes, immune cells, immune-related genes and LVI-associated differential GO items and KEGG pathways were analyzed. A random forest (RF) and eXtreme Gradient Boosting (XGB) model were constructed to predict the LVI of CRC patients based on the differential microbiome.<br><br>RESULT: There was no significant difference in &#x3b1;-diversity and &#x3b2;-diversity of intestinal microbiome between CRC patients with and without LVI (P > 0.05). Linear discriminant analysis Effect Size (LEfSe) analysis showed 34 intestinal microbiomes enriched in CRC patients of the LVI group and 5 intestinal microbiomes were significantly enriched in CRC patients of the non-lymph-vascular invasion (NLVI) group. The RF and XGB prediction models constructed with the top 15% of the LVI-associated differential intestinal microbiomes ranked by feature significance had good efficacy.<br><br>CONCLUSIONS: There are 39 intestinal flora with significantly different species abundance between the LVI and NLVI groups. g:Alistipes.s:Alistipes_indistinctus is closely associated with colorectal cancer vascular invasion. LVI-associated differential intestinal flora may be involved in regulating the infiltration of immune cells in CRC and influencing the expression of immune-related genes. LVI-associated differential intestinal flora may influence the process of vascular invasion in CRC through a number of potential biological functions. RF prediction models and XGB prediction models constructed based on microbial markers of gut flora can be used to predict CRC-LVI conditions.}, }
@article {pmid37249977, year = {2023}, author = {Li, Z and Fu, R and Huang, X and Wen, X and Zhang, L}, title = {A decade of progress: bibliometric analysis of trends and hotspots in oral microbiome research (2013-2022).}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1195127}, pmid = {37249977}, issn = {2235-2988}, abstract = {BACKGROUND: Over the past decade, a plethora of studies have delved into the oral microbiome. Our objective was to evaluate the trends in oral microbiome research employing a quantitative approach.<br><br>MATERIALS AND METHODS: We extracted clinical studies on the oral microbiome published between 2013 and 2022 from the Web of Science database, yielding 3024 articles. The assembled literature was visually scrutinized using VOSviewer 1.6.18, Citespace 6.1.6, Pajek, Scimago Graphica, and other specialized software to assess authors, institutions, countries, journals, co-cited literature, keywords, genes, and diseases.<br><br>RESULTS: Our analysis identified a total of 3024 articles. The volume and rate of annual publications steadily increased, with research interest in the oral microbiome progressively intensifying. The United States, China, and the UK contributed the highest number of publications. Growth rates of publications varied among countries over time. The Forsyth Institute emerged as the most collaborative institution, boasting the highest number of relevant papers (135) and securing the top rank, followed by Sichuan University and Harvard University. Paster Bruce J, Zhou Xuedong, and He Xuesong were pioneers in the field of oral microbiome research. This analysis demonstrates that the homeostatic balance of the oral microbiome, advanced microbial sequencing technology, connections with gut microbiota, and tumorigenesis, including oral cancer, have become emerging topics in the oral microbiome field.<br><br>CONCLUSIONS: This study delineated a comprehensive landscape of hotspots and frontiers in oral microbiome research, thus facilitating the identification of interdisciplinary advancements. We sincerely hope that our bibliometric analysis will enable researchers to leverage the oral microbiome to ultimately improve human oral health.}, }
@article {pmid37249910, year = {2023}, author = {Margolis, EB and Alfaro, GM and Sun, Y and Dallas, RH and Allison, KJ and Ferrolino, J and Ross, HS and Davis, AE and Jia, Q and Turner, P and Mackay, V and Morin, CE and Triplett, BM and Klein, EJ and Englund, JA and Tang, L and Hayden, RT}, title = {Microbiota Predict Infections and Acute Graft-Versus-Host Disease after Pediatric Allogeneic Hematopoietic Stem Cell Transplantation.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiad190}, pmid = {37249910}, issn = {1537-6613}, abstract = {BACKGROUND: Despite intensive prophylactic and pre-emptive measures, infections remain an important cause of morbidity and mortality in pediatric recipients of allogeneic hematopoietic cell transplantation (allo-HCT). Disruption of the gut microbiota has been linked to clinical outcomes after adult allo-HCT. This study evaluated whether these or differing microbiota disruptions or signatures were associated with risk of infection in pediatric allo-HCT.<br><br>METHODS: In a prospective observational study, fecal samples from 74 children were collected prior to conditioning and at the time of neutrophil recovery and profiled by means of 16S ribosomal rRNA sequencing. The associations between microbiome signatures and infections or acute graft-versus-host disease (aGVHD) were examined using Cox proportional-hazards analysis.<br><br>RESULTS: Previously associated indices of microbiome disruption in adults, including diversity and butyrate producer frequency, did not predict infection risk in pediatric allo-HCT. Unique microbiota signatures were associated with different infections or aGVHD. A ratio of strict and facultative anaerobes (e.g. Lachnoclostridium, Parabacteroides, Clostridium spp.) prior to conditioning predicted likelihood of bacteremia (cox hazards ratio 3.89) in first year post HCT. A distinct ratio of oral (e.g. Rothia, Veillonella spp.) to colonic anaerobes (e.g. Anaerobutyricum, Dorea, Romboutsia spp.) at neutrophil recovery predicted likelihood of bacterial infections (cox hazards ratio 1.81) and viral enterocolitis (cox hazards ratio 1.96) through first year post transplant.<br><br>CONCLUSIONS: Interactions between medical interventions, pediatric hosts and microbial communities may be responsible for these consistent microbiota signatures that predict infections. A future multi-center investigation will be needed to demonstrate whether these ratios can be generalized to other pediatric cohorts.}, }
@article {pmid37249755, year = {2023}, author = {Vanoli, A and Parente, P and Fassan, M and Mastracci, L and Grillo, F}, title = {Gut inflammation and tumorigenesis: every site has a different tale to tell.}, journal = {Internal and emergency medicine}, volume = {}, number = {}, pages = {}, pmid = {37249755}, issn = {1970-9366}, abstract = {Gut inflammation has been correlated with cancerogenesis by disrupting gastrointestinal homeostasis. Numerous chronic inflammatory disorders of the tubular gastrointestinal tract (e.g., gastroesophageal reflux disease, Helicobacter pylori-induced and autoimmune chronic gastritis, celiac disease, and inflammatory bowel diseases) have been variably associated with an increased neoplastic risk. Gastrointestinal inflammation-induced neoplasms include epithelial tumors (esophageal squamous cell carcinoma and adenocarcinoma, gastric adenocarcinoma and neuroendocrine tumors, small bowel adenocarcinoma and neuroendocrine tumors, and colorectal cancer) and lymphomas (such as gastric marginal zone lymphomas and enteropathy-associated T cell lymphoma). In the last decades, numerous studies have investigated the pathogenetic mechanisms and the microenvironmental/microbiome changes that trigger genetic and/or epigenetic alterations eventually leading to tumorigenesis, often through a histologically recognizable inflammation-dysplasia-carcinoma cancerogenic sequence. In the present review, an overview of the current knowledge on the links between inflammatory diseases and neoplasms of the tubular GI tract, applying a site-by-site approach, is provided.}, }
@article {pmid37249591, year = {2023}, author = {Wu-Chuang, A and Hartmann, D and Maitre, A and Mateos-Hernández, L and Frantová, H and Urbanová, V and Obregon, D and Cabezas-Cruz, A and Perner, J}, title = {Variation of bacterial community assembly over developmental stages and midgut of Dermanyssus gallinae.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37249591}, issn = {1432-184X}, abstract = {Bacterial microbiota play an important role in the fitness of arthropods, but the bacterial microflora in the parasitic mite Dermanyssus gallinae is only partially explored; there are gaps in our understanding of the microbiota localization and in our knowledge of microbial community assembly. In this work, we have visualized, quantified the abundance, and determined the diversity of bacterial occupancy, not only across developmental stages of D. gallinae, but also in the midgut of micro-dissected female D. gallinae mites. We explored community assembly and the presence of keystone taxa, as well as predicted metabolic functions in the microbiome of the mite. The diversity of the microbiota and the complexity of co-occurrence networks decreased with the progression of the life cycle. However, several bacterial taxa were present in all samples examined, indicating a core symbiotic consortium of bacteria. The relatively higher bacterial abundance in adult females, specifically in their midguts, implicates a function linked to the biology of D. gallinae mites. If such an association proves to be important, the bacterial microflora qualifies itself as an acaricidal or vaccine target against this troublesome pest.}, }
@article {pmid37249474, year = {2023}, author = {Sheng, Y and Meng, G and Zhou, Z and Du, R and Wang, Y and Jiang, M}, title = {PARP-1 inhibitor alleviates liver lipid accumulation of atherosclerosis via modulating bile acid metabolism and gut microbes.}, journal = {Molecular omics}, volume = {}, number = {}, pages = {}, doi = {10.1039/d3mo00033h}, pmid = {37249474}, issn = {2515-4184}, abstract = {Background: The DNA damage repair enzyme, poly(ADP-ribose) polymerase 1 (PARP1), is crucial for lipid and glucose metabolism. However, no evidence has been presented on the relationship between liver lipid accumulation and the PARP1 inhibitor, 3-aminobenzamide (3-AB), in atherosclerosis. Methods: ApoE[-/-] mice were used to explore the effect of 3-AB on atherosclerotic liver lipid accumulation, and the experiment of Sprague Dawley (SD) rats was designed to determine if the lowering of liver lipid levels by 3-AB was linked to gut bacteria. The levels of bile acid metabolism-related targets were assessed by ELISA, western blotting, and RT-qPCR. The relative abundances of gut microbes and biomarkers were determined using 16S rRNA sequencing analysis. Bile acid levels in the liver and ileum were examined by ultra-performance liquid chromatography-tandem mass spectrometry. The relationship between gut microbes and bile acids was assessed by Spearman's correlation analysis. Results: 3-AB significantly reduced the formation of aortic plaques in apoE[-/-] mice, according to gross oil red staining. H &amp; E and Oil Red O staining revealed that 3-AB significantly reduced the hepatic lipid droplet area in ApoE[-/-] mice and SD rats. Compared with the atherosclerosis (ATH) group, 3-AB dramatically decreased the levels of total cholesterol (TC), triglyceride (TG), and low-density lipoprotein-cholesterol (LDL-C) in the serum of SD rats and apoE[-/-] mice, and the levels of TC, TG, and LDL-C in the serum and liver of apoE[-/-] mice. Furthermore, in apoE[-/-] mice and SD rats, 3-AB increased the mRNA and protein levels of farnesoid X receptor (FXR) and bile salt export pump (BSEP) in the liver, while inhibiting the mRNA and protein levels of FXR and fibroblast growth factor 15 (FGF15) in the ileum, respectively. 3-AB clearly inhibited the mRNA and protein levels of PARP1 in the liver and ileum of apoE[-/-] mice and rats. Following treatment with 3-AB, the levels of conjugated bile acids decreased in the liver of apoE[-/-] mice and increased in the ileum of SD rats, according to targeted metabolomic analysis. Microbiome sequencing analysis revealed that 3-AB reduced the relative abundance of Lactobacillus, Bifidobacterium, Listeria, Clostridium, Bacillus, and Staphylococcus in the feces of apoE[-/-] mice, and the relative abundance of Blautia, Clostridium, and Listeria in the feces of SD rats, eventually decreasing the total abundance of 10 bile salt hydrolase-associated gut microbes. According to the correlation analysis, 3-AB regulates bile acid metabolism, which is primarily related to Bifidobacterium. Conclusion: 3-AB alleviated atherosclerosis by modulating the bile acid metabolism and bile salt hydrolase-related gut microbes.}, }
@article {pmid37249298, year = {2023}, author = {Luiten, D and Biezeveld, M and van Doorn, O and Riady, H and Yang, M and Bergsma, F and van der Plas, A and Brand, K and Arends, N and de Bruin, A and de Vries, J and de Meij, T and Vlieg-Boerstra, B}, title = {Peanut thresholds in peanut-allergic children are related to dietary composition.}, journal = {Immunity, inflammation and disease}, volume = {11}, number = {5}, pages = {e841}, doi = {10.1002/iid3.841}, pmid = {37249298}, issn = {2050-4527}, abstract = {BACKGROUND: There is no clear explanation for the large variation in threshold levels among peanut-allergic children. We hypothesized that diet composition can partly explain this variation in thresholds, as nutrients and foods influence the intestinal barrier function and microbiota.<br><br>AIM: to explore the relationship between the threshold levels for peanut and nutritional intake and gut microbial composition in peanut-allergic children.<br><br>METHODS: In this explorative cross-sectional study the cumulative threshold levels for peanut were determined by oral food challenge tests. Data on nutrients and foods consumed were obtained from 3-day food diaries. Microbial composition of faeces and saliva were determined by molecular microbiota detection technique. Multivariable linear regression analysis and multiple logistic regression were used to explore the associations, adjusted for energy and senitization.<br><br>RESULTS: Sixty-five children were included, of whom 32 (49%) (median age 50 months, IQR 28.0-96.5) had a positive oral food challenge. Significant positive associations were found between the intake of total carbohydrates, vitamin A and cumulative threshold levels for peanut, while significant negative associations were found for long-chain polyunsaturated fatty acids, linoleic acid and omega-6 fatty acids. No associations were found between threshold levels and microbial composition of faeces and saliva. However, a significant higher abundance of Proteobacteria and Bacteroidetes in saliva (p&#x2009;=&#x2009;0.011 and 0.04, respectively) and of Proteobacteria in faeces (p&#x2009;=&#x2009;0.003) were found in children with a positive peanut challenge compared to children with a negative peanut challenge.<br><br>CONCLUSION: As a novel concept, this study showed that dietary composition is related to threshold levels for peanut.}, }
@article {pmid37249085, year = {2023}, author = {Ting, HSL and Chen, Z and Chan, JYK}, title = {Systematic review on oral microbial dysbiosis and its clinical associations with head and neck squamous cell carcinoma.}, journal = {Head &amp; neck}, volume = {}, number = {}, pages = {}, doi = {10.1002/hed.27422}, pmid = {37249085}, issn = {1097-0347}, abstract = {OBJECTIVES: The relationship between head and neck squamous cell carcinoma (HNSCC) and the oral microbiome has been drawn in various studies. Microbial diversities, microbiome profiles, metagenomic analysis, and host-pathogen interactions were collected from these studies to highlight similarities and account for inconsistencies. We also evaluate the possible clinical applications of the microbiome regarding screening and diagnosis of HNSCC.<br><br>METHODS: Systematic analysis of studies regarding HNSCC and the microbiome was done according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement guidelines. Articles were retrieved from four databases (PubMed, ScienceDirect, CUHK Full-Text Journals, and Cochrane database) and were screened using predefined criteria.<br><br>RESULTS: Twenty studies were chosen after screening for full-text review. &#x3b1;-diversity comparison was inconsistent whereas &#x3b2;-diversity between HNSCC and normal samples showed distinct clustering. Microbial dysbiosis characterized by change in the relative abundances of several bacterial species were also seen in HNSCC patients. At a phylum level, inconsistencies were seen between studies using HNSCC tumor tissue samples and saliva samples. At a genus level, Fusobacterium, Peptostreptococcus, Alloprevotella, Capnocytophaga, Catonella, and Prevotella were differentially enriched in HNSCC while Streptococcus, Actinomyces Veillonella, and Rothia were differentially depleted. Co-occurrence network analysis revealed a positive correlation of HNSCC with periodontal pathogens and a negative correlation with commensal bacteria. Metagenomic analysis of microbiota revealed a differential enrichment of pro-inflammatory genomic pathways which was consistent across various studies. Microbial dysbiosis was applied in clinical use as a tool for HNSCC screening. Random-forest analysis was adopted to differentiate between tumor and normal tissue, at 95.7% and 70.0% accuracies respectively in two studies. Microbial dysbiosis index was also used to predict prognosis.<br><br>CONCLUSIONS: Oral microbial dysbiosis could be a promising tool for HNSCC screening and diagnosis. However, more research should be conducted pertaining to clinical applications to improve diagnostic accuracy and explore other clinical uses.}, }
@article {pmid37249060, year = {2023}, author = {Wolf, M and Schallert, K and Knipper, L and Sickmann, A and Sczyrba, A and Benndorf, D and Heyer, R}, title = {Advances in the clinical use of metaproteomics.}, journal = {Expert review of proteomics}, volume = {}, number = {}, pages = {1-16}, doi = {10.1080/14789450.2023.2215440}, pmid = {37249060}, issn = {1744-8387}, abstract = {INTRODUCTION: Investigating the taxonomic and functional composition of human microbiomes can aid in the understanding of disease etiologies, diagnosis, and therapy monitoring for several diseases, including inflammatory bowel disease or obesity. One method for microbiome monitoring is metaproteomics, which assesses human and microbial proteins and thus enables the study of host-microbiome interactions. This advantage led to increased interest in metaproteome analyses and significant developments to introduce this method into a clinical context.<br><br>AREAS COVERED: This review summarizes the recent progress from a technical side and an application-related point of view.<br><br>EXPERT OPINION: Numerous publications imply the massive potential of metaproteomics to impact human health care. However, the key challenges of standardization and validation of experimental and bioinformatic workflows and accurate quantification methods must be overcome.}, }
@article {pmid37248617, year = {2023}, author = {Fields, B and Moeskjaer, S and Deakin, WJ and Moffat, EK and Roulund, N and Andersen, SU and Young, JPW and Friman, VP}, title = {Rhizobium nodule diversity and composition are influenced by clover host selection and local growth conditions.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.17028}, pmid = {37248617}, issn = {1365-294X}, abstract = {While shaping of plant microbiome composition through 'host filtering' is well documented in legume-rhizobium symbioses, it is less clear to what extent different varieties and genotypes of the same plant species differentially influence symbiont community diversity and composition. Here, we compared how clover host varieties and genotypes affect the structure of Rhizobium populations in root nodules under conventional field and controlled greenhouse conditions. We first grew four Trifolium repens (white clover) F2 crosses and one variety in a conventional field trial and compared differences in root nodule Rhizobium leguminosarum symbiovar trifolii (Rlt) genotype diversity using high-throughput amplicon sequencing of chromosomal housekeeping (rpoB and recA) genes and auxiliary plasmid-borne symbiosis genes (nodA and nodD). We found that Rlt nodule diversities significantly differed between clover crosses, potentially due to host filtering. However, variance in Rlt diversity largely overlapped between crosses and was also explained by the spatial distribution of plants in the field, indicative of the role of local environmental conditions for nodule diversity. To test the effect of host filtering, we conducted a controlled greenhouse trial with a diverse Rlt inoculum and several host genotypes. We found that different clover varieties and genotypes of the same variety selected for significantly different Rlt nodule communities and that the strength of host filtering (deviation from the initial Rhizobium inoculant composition) was positively correlated with the efficiency of symbiosis (rate of plant greenness colouration). Together, our results suggest that selection by host genotype and local growth conditions jointly influence white clover Rlt nodule diversity and community composition.}, }
@article {pmid37248575, year = {2023}, author = {Peng, YM and Luo, XM and Chen, JY}, title = {[Research Progress and New Immunotherapy Strategies of Tumor Microenvironment Metabolism].}, journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition}, volume = {54}, number = {3}, pages = {505-509}, doi = {10.12182/20230560502}, pmid = {37248575}, issn = {1672-173X}, abstract = {The tumor microenvironment (TME), the environment of tumorigenesis and tumor progression, incorporates multiple types of cells and non-cellular components. TME plays an important role in tumorigenesis and tumor progression. Due to the abnormal proliferation of tumors, the TME has a unique chemophysiology environment and complex metabolic patterns, which subsequently affects the role of immune cells. Understanding the metabolic patterns of TME can help us develop immunotherapy regimens that target TME. Microbial metabolism and lipid metabolism, the key metabolic processes of TME, have emerged as important foci of research. The metabolites released by the microbiome and the reprogramming of cellular lipid metabolism affect the subsistence of tumor and immune cells. In this review, we summarized the composition and metabolic characteristics of TME and discussed the latest research progress in microbial metabolism and lipid metabolism in TME. We also provided an update on relevant metabolic regulatory targets and immunotherapy strategies, stressing that identifying highly effective therapeutic targets, in spite of the apparent difficulty, is what future research should be focused on.}, }
@article {pmid37248173, year = {2023}, author = {Lee, CH and Koh, SJ and Radi, ZA and Habtezion, A}, title = {Animal models of inflammatory bowel disease: novel experiments for revealing pathogenesis of colitis, fibrosis, and colitis-associated colon cancer.}, journal = {Intestinal research}, volume = {}, number = {}, pages = {}, doi = {10.5217/ir.2023.00029}, pmid = {37248173}, issn = {1598-9100}, abstract = {Inflammatory bowel disease (IBD), comprising Crohn's disease and ulcerative colitis, is a lifelong disease that manifests with chronic intestinal inflammation, sequential fibrosis, and an increased risk of colitis-associated colon cancer (CAC). The combined effects of genetic, immunological, environmental, and microbial factors render it difficult to determine the specific mechanism underlying the induction and perpetuation of IBD. Various animal models of IBD have contributed enormously to the understanding of IBD pathogenesis in terms of genomics, transcriptomics, proteomics, microbiome, and drug development of novel therapeutics. Although comprehensive research on IBD has been enabled by advanced technologies, such as genetically engineered models, there is a great need to develop relevant in vivo models of colitis and fibrosis. Here, we review 4 categories of animal models of acute and chronic intestinal inflammation, fibrosis, and CAC: chemically induced, genetically engineered, T cell transfer, and spontaneous gene mutation models.}, }
@article {pmid37247806, year = {2023}, author = {Karandikar, K and Bhonde, G and Palav, H and Padwal, V and Velhal, S and Pereira, J and Meshram, H and Goel, A and Shah, I and Patel, V and Bhor, VM}, title = {A Novel Gut Microbiome-Immune Axis influencing pathology in HCMV Infected Infants with Neonatal Cholestasis.}, journal = {Microbes and infection}, volume = {}, number = {}, pages = {105165}, doi = {10.1016/j.micinf.2023.105165}, pmid = {37247806}, issn = {1769-714X}, abstract = {The interplay of active HCMV infection with gut dysbiosis in the immunopathology of cholestasis in neonates and infants remains unexplored. In this study, we evaluated gut microbiome profiles and immune dysfunction in a cohort of HCMV infected cholestatic infants (IgM positive, N=21; IgM negative, N= 25) compared to healthy infants, N=10. HCMV infected IgM positive individuals exhibited increased clinical severity in terms of liver dysfunction, altered CD4[+]: CD8[+] ratio, and elevated Granzyme B levels in cellular immune subsets. Gut microbiome analysis revealed distinct and differential diversity and composition within infected groups aligned with clinical severity reflected through the increased abundance of Gammaproteobacteria, reduced Bifidobacteria, and a unique signature mapping to the HCMV infected IgM negative group. Correlation analyses revealed associations between Bifidobacterium breve, Gammaproteobacteria, Firmicutes, Clostridia, Finegoldia magna, Veillonella dispar, and Granzyme B expressing immune cell subsets. Our study describes a novel gut microbiome-immune axis that may influence disease severity in cholestatic infants with active HCMV infection.}, }
@article {pmid37247742, year = {2023}, author = {Maguire, LW and Gardner, CM}, title = {Fate and transport of biological microcontaminants bound to microplastics in the soil environment.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164439}, doi = {10.1016/j.scitotenv.2023.164439}, pmid = {37247742}, issn = {1879-1026}, abstract = {Microplastics, fragmented plastic particles with a maximum dimension <5 mm, are an emerging contaminant of concern that can also serve as a vector of other chemical and biological contaminants. Compared to chemical contaminants, the potential of microplastics to adsorb biological microcontaminants such as antibiotic resistance genes, small interference RNAs, and pathogenic viruses is not well understood. Many current microplastic studies are based in the aquatic environment (freshwater, seawater, and wastewater), even though the terrestrial environment is considered both an important sink and source of microplastics. Microplastics co-occur with biological microcontaminants in many terrestrial environments including agricultural soils, where biosolids containing both contaminants are often applied as a soil amendment. Recent research suggests that microplastics in these environments can increase gene persistence and flow, which could have unintended downstream consequences for environmental microbiome health and resilience. Antibiotic resistance genes and silencing RNAs bound to microplastics, for example, have the potential to increase resistance and alter gene expression in environmental bacteria, respectively. This review evaluates the sources and pathways of microplastics and biological microcontaminants in the terrestrial environment as well as potential sorption mechanisms that can encourage long-range transport and persistence. Novel sources of biological microcontaminants are considered, and the role of microplastics in promoting the persistence and flow of biological microcontaminants evaluated. Finally, future research directions are suggested to increase understanding of the mechanisms that drive the fate and transport of microplastic-biological microcontaminant complexes in the terrestrial environment and better inform risk management.}, }
@article {pmid37247671, year = {2023}, author = {Wang, Z and Li, Q and Huang, H and Liu, J and Wang, J and Chen, Y and Huang, S and Luo, X and Zheng, Z}, title = {Distribution and potential ecological risks of microplastics in Zhushan Bay, China.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {139024}, doi = {10.1016/j.chemosphere.2023.139024}, pmid = {37247671}, issn = {1879-1298}, abstract = {The interaction between microplastics (MPs) and microorganisms may alter the distribution of antibiotic resistance genes (ARGs) in water and increase the ecological risk of drinking water sources. To investigate the characteristics of MPs geographical distribution and its potential ecological risk in typical urban water, this study was conducted in Zhushan Bay, and we carried out a combination of tests to analyze the distribution of MPs and the migration changes of their surface microbial community composition and ARGs in different media by 16S rRNA gene high-throughput sequencing, non-targeted metabolomics and qPCR genomics in the near-shore (I), middle area (Ⅱ) and near-lake (Ⅲ) of Zhushan Bay. The results showed that MPs in fibrous form were dominant in the aquatic environment of Zhushan Bay; Polyurethane (PU) and Silicone were the main MPs types in Zhushan Bay. The abundance of MPs in the water of Zhushan Bay was winter > summer > autumn > spring; and in the sediment was winter > summer > autumn > spring, respectively. The distribution results of MPs in geographical location are as follows: In the water I > Ⅱ > Ⅲ, sediment exhibited Ⅱ > Ⅲ > I. The results indicate that physicochemical factors will affect the geographical distribution of MPs and their surface microbial community composition in the aquatic environment of Zhushan Bay. More cooperative behaviors and increased metabolically important pathways occurred in the microbial network on water-MPs compared to sediment-MPs. However, the microbial community in the sediment-MPs was more stable and had higher abundance of mobile genetic elements (MGEs). A total of 362 differential metabolites were detected, of which 193 were up-regulated and 19 down-regulated differential metabolites. blaTEM, Sul, and inti1 were prevalent in both the water and sediments of Zhushan Bay. Sul1 was most contaminated in ARGs. This study provides the latest field data and insights into MPs pollution in key aquatic environments.}, }
@article {pmid37247575, year = {2023}, author = {Sun, W and Dang, Y and Dai, L and Liu, C and Wang, J and Guo, Y and Fan, B and Kong, J and Zhou, B and Ma, X and Yu, L}, title = {Tris(1,3-dichloro-2-propyl) phosphate causes female-biased growth inhibition in zebrafish: Linked with gut microbiota dysbiosis.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {260}, number = {}, pages = {106585}, doi = {10.1016/j.aquatox.2023.106585}, pmid = {37247575}, issn = {1879-1514}, abstract = {Tris(1,3-dichloro-2-propyl) phosphate (TDCIPP) is ubiquitous in aquatic environment, but its effect on intestinal health of fish has yet not been investigated. In the present study, the AB strain zebrafish embryos were exposed to environmentally realistic concentrations (0, 30, 300, and 3000 ng·L[-1]) of TDCIPP for 90 days, after which the fish growth and physiological activities were evaluated, and the intestinal microbes were analyzed by 16S rRNA gene high-throughput sequencing. Our results manifested that the body length and body weight were significantly reduced in the female zebrafish but not in males. Further analyses revealed that TDCIPP resulted in notable histological injury of intestine, which was accompanied by impairment of epithelial barrier integrity (decreased tight junction protein 2), inflammation responses (increased interleukin 1β), and disruption of neurotransmission (increased serotonin) in female intestine. Male intestines maintained intact intestinal structure, and the remarkably increased activity of glutathione peroxidase (GPx) might protect the male zebrafish from inflammation and intestinal damage. Furthermore, 16S rRNA sequencing analysis showed that TDCIPP significantly altered the microbial communities in the intestine in a gender-specific manner, with a remarkable increase in alpha diversity of the gut microbiome in male zebrafish, which might be another mechanism for male fish to protect their intestines from damage by TDCIPP. Correlation analysis revealed that abnormal abundances of pathogenic bacteria (Chryseobacterium, Enterococcus, and Legionella) might be partially responsible for the impaired epithelial barrier integrity and inhibition in female zebrafish growth. Taken together, our study for the first time demonstrates the high susceptibility of intestinal health and gut microbiota of zebrafish to TDCIPP, especially for female zebrafish, which could be partially responsible for the female-biased growth inhibition.}, }
@article {pmid37246806, year = {2023}, author = {Harder, I and Stölzl, D and Sander, N and Hartmann, J and Rodriguez, E and Mazur, C and Kerzel, S and Kabesch, M and Küster, D and Schmitt, J and Fölster-Holst, R and Gerdes, S and Emmert, H and Weidinger, S}, title = {Effects of Early Emollient Use in Children at High Risk of Atopic Dermatitis: A German Pilot Study.}, journal = {Acta dermato-venereologica}, volume = {103}, number = {}, pages = {adv5671}, doi = {10.2340/actadv.v103.5671}, pmid = {37246806}, issn = {1651-2057}, mesh = {Child ; Humans ; Infant ; Infant, Newborn ; *Dermatitis, Atopic/diagnosis/drug therapy/prevention &amp; control ; *Emollients/adverse effects ; Pilot Projects ; Skin ; Skin Physiological Phenomena ; Treatment Outcome ; }, abstract = {Several small studies have indicated that daily emollient use from birth might delay, suppress or prevent atopic dermatitis (AD). Two larger trials did not confirm this; however, a recent smaller study indicated a protective effect if daily emollient use is used in the first 2 months of life. Further research is needed to evaluate the effect of emollient use on development of AD. The current study randomly assigned 50 newborns who were at high risk of developing AD (1:1) to receive general infant skin-care advice (control group), or skin-care advice plus emollient with advice to apply emollient at least once daily until 1 year of age (intervention group). Repeated skin examinations, skin physiology measurements and skin microbiome profiling were performed. Of the children in the intervention and control groups, 28% and 24%, respectively, developed AD (adjusted Relative Risk (RR) 1.19, p = 0.65, adjusted risk difference 0.05). Skin pH decreased and transepidermal water loss and stratum corneum hydration increased over time in both groups with no significant differences. In the intervention group skin microbiome alpha diversity increased earlier, and the abundance of Streptococcus and Staphylococcus species were significantly reduced at month 1. Daily early emollient use in children with high risk of AD was safe, but it did not significantly reduce the risk of developing AD or impact skin physiology development.}, }
@article {pmid37246607, year = {2023}, author = {Antonyuk, SV and Siemińska, K and Śmiga, M and Strange, RW and Wagner, M and Barnett, KJ and Olczak, T}, title = {Bacteroides fragilis expresses three proteins similar to Porphyromonas gingivalis HmuY: Hemophore-like proteins differentially evolved to participate in heme acquisition in oral and gut microbiomes.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {37}, number = {7}, pages = {e22981}, doi = {10.1096/fj.202300366R}, pmid = {37246607}, issn = {1530-6860}, mesh = {Humans ; *Porphyromonas gingivalis ; Bacteroides fragilis/genetics/metabolism ; *Gastrointestinal Microbiome ; Dysbiosis ; Heme/metabolism ; Bacterial Proteins/metabolism ; }, abstract = {Oral and gut microbiomes are important for the maintenance of homeostasis in the human body. Altered or disturbed mutualism between their members results in dysbiosis with local injury and subsequent systemic diseases. The high bacterial density causes intense competition among microbiome residents to acquire nutrients, including iron and heme, the latter of high importance for heme auxotrophic members of the Bacteroidetes phylum. Our main hypothesis is that the heme acquisition mechanism, with the leading role played by a novel HmuY family of hemophore-like proteins, can be used to fulfill nutritional requirements and increase virulence. We characterized HmuY homologs expressed by Bacteroides fragilis and compared their properties with the first representative of this family, the HmuY protein of Porphyromonas gingivalis. In contrast to other Bacteroidetes members, B. fragilis produces three HmuY homologs (Bfr proteins). All bfr transcripts were produced at higher levels in bacteria starved of iron and heme (fold change increase ~60, ~90, and ~70 for bfrA, bfrB, and bfrC, respectively). X-ray protein crystallography showed that B. fragilis Bfr proteins are structurally similar to P. gingivalis HmuY and to other homologs, except for differences in the potential heme-binding pockets. BfrA binds heme, mesoheme, and deuteroheme, but preferentially under reducing conditions, using Met175 and Met146 to coordinate heme iron. BfrB binds iron-free protoporphyrin IX and coproporphyrin III, whereas BfrC does not bind porphyrins. HmuY is capable of heme sequestration from BfrA, which might increase the ability of P. gingivalis to cause dysbiosis also in the gut microbiome.}, }
@article {pmid37246455, year = {2023}, author = {Le, D and Chambers, MM and Mercado, K and Gutowski, CJ}, title = {Characterization of the Gut Microbiome in an Osteosarcoma Mouse Model.}, journal = {Journal of orthopaedic research : official publication of the Orthopaedic Research Society}, volume = {}, number = {}, pages = {}, doi = {10.1002/jor.25635}, pmid = {37246455}, issn = {1554-527X}, abstract = {Compelling evidence has mounted surrounding the relationship between the gut microbiome and many intestinal and extraintestinal cancers. Few studies exist investigating the relationship between the gut microbiome and sarcoma. We hypothesize that the presence of distant osteosarcoma induces change to the profile of flora within the mouse. Twelve mice were used for this experiment: six were sedated and received an injection of human osteosarcoma cells into the flank, while six served as controls. Baseline stool and weight were collected. Tumor size and mouse weight were recorded weekly while stool samples were collected daily. Fecal microbiomes of the mice were profiled by 16S rRNA gene sequencing and analyzed for alpha, relative abundances of microbial taxa, and abundance of specific bacteria at different time points. Alpha diversity was increased in the osteosarcoma group compared to the control group. The family Lachnospiraceae had the second strongest negative net average change in relative abundance over time in the osteosarcoma group whereas it had a positive net average change in the control group. An increased Firmicutes to Bacteroidota (F/B) ratio was observed in the osteosarcoma group relative to the control mice. These differences suggest that there may be an interplay between the gut microbiome and osteosarcoma. This article is protected by copyright. All rights reserved.}, }
@article {pmid37246304, year = {2023}, author = {Arredondo, A and Àlvarez, G and Isabal, S and Teughels, W and Laleman, I and Contreras, MJ and Isbej, L and Huapaya, E and Mendoza, G and Mor, C and Nart, J and Blanc, V and León, R}, title = {Comparative 16S rRNA gene sequencing study of subgingival microbiota of healthy subjects and patients with periodontitis from four different countries.}, journal = {Journal of clinical periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jcpe.13827}, pmid = {37246304}, issn = {1600-051X}, abstract = {AIM: To investigate the differences between the subgingival microbiota of healthy subjects (HS) and periodontitis patients (PP) from four different countries through a metagenomic approach.<br><br>MATERIALS AND METHODS: Subgingival samples were obtained from subjects from four different countries. Microbial composition was analysed through high-throughput sequencing of the V3-V4 region of the 16S rRNA gene. The country of origin, diagnosis and clinical and demographic variables of the subjects were used to analyse the microbial profiles.<br><br>RESULTS: In total, 506 subgingival samples were analysed: 196 from HS and 310 from patients with periodontitis. Differences in richness, diversity and microbial composition were observed when comparing samples pertaining to different countries of origin and different subject diagnoses. Clinical variables, such as bleeding on probing, did not significantly affect the bacterial composition of the samples. A highly conserved core of microbiota associated with periodontitis was detected, while the microbiota associated with periodontally HS was much more diverse.<br><br>CONCLUSIONS: Periodontal diagnosis of the subjects was the main variable explaining the composition of the microbiota in the subgingival niche. Nevertheless, the country of origin also had a significant impact on the microbiota and is therefore an important factor to consider when describing subgingival bacterial communities.}, }
@article {pmid37246133, year = {2023}, author = {Wu, R and Xiong, R and Li, Y and Chen, J and Yan, R}, title = {Gut microbiome, metabolome, host immunity associated with inflammatory bowel disease and intervention of fecal microbiota transplantation.}, journal = {Journal of autoimmunity}, volume = {}, number = {}, pages = {103062}, doi = {10.1016/j.jaut.2023.103062}, pmid = {37246133}, issn = {1095-9157}, abstract = {Gut dysbiosis has been associated with inflammatory bowel disease (IBD), one of the most common gastrointestinal diseases. The microbial communities play essential roles in host physiology, with profound effects on immune homeostasis, directly or via their metabolites and/or components. There are increasing clinical trials applying fecal microbiota transplantation (FMT) with Crohn's disease (CD) and ulcerative colitis (UC). The restoration of dysbiotic gut microbiome is considered as one of the mechanisms of FMT therapy. In this work, latest advances in the alterations in gut microbiome and metabolome features in IBD patients and experimental mechanistic understanding on their contribution to the immune dysfunction were reviewed. Then, the therapeutic outcomes of FMT on IBD were summarized based on clinical remission, endoscopic remission and histological remission of 27 clinical trials retrieved from PubMed which have been registered on ClinicalTrials.gov with the results been published in the past 10 years. Although FMT is established as an effective therapy for both subtypes of IBD, the promising outcomes are not always achieved. Among the 27 studies, only 11 studies performed gut microbiome profiling, 5 reported immune response alterations and 3 carried out metabolome analysis. Generally, FMT partially restored typical changes in IBD, resulted in increased α-diversity and species richness in responders and similar but less pronounced shifts of patient microbial and metabolomics profiles toward donor profiles. Measurements of immune responses to FMT mainly focused on T cells and revealed divergent effects on pro-/anti-inflammatory functions. The very limited information and the extremely confounding factors in the designs of the FMT trials significantly hindered a reasonable conclusion on the mechanistic involvement of gut microbiota and metabolites in clinical outcomes and an analysis of the inconsistencies.}, }
@article {pmid37246076, year = {2023}, author = {Lotti, S and Dinu, M and Colombini, B and Amedei, A and Sofi, F}, title = {Circadian rhythms, gut microbiota, and diet: Possible implications for health.}, journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.numecd.2023.05.009}, pmid = {37246076}, issn = {1590-3729}, abstract = {AIMS: Over the past years, interest in chrono-nutrition has grown enormously as the fundamental role of circadian rhythms in regulating most physiological and metabolic processes has become clearer. Recently, the influence of circadian rhythms on the gut microbiota (GM) composition has also emerged, as more than half of the total microbial composition fluctuates rhythmically throughout the day. At the same time, other studies have observed that the GM itself synchronises the host's circadian biological clock through signals of a different nature. Therefore, it has been hypothesised that there is a two-way communication between the circadian rhythms of the host and the GM, but researchers have only just begun to identify some of its action mechanisms. The manuscript aim is, therefore, to gather and combine the latest evidence in the field of chrono-nutrition with the more recent research on the GM, in order to investigate their relationship and their potential impact on human health.<br><br>DATA SYNTHESIS: Considering current evidence, a desynchronization of circadian rhythms is closely associated with an alteration in the abundance and functionality of the gut microbiota with consequent deleterious effects on health, such as increased risk of numerous pathologies, including cardiovascular disease, cancer, irritable bowel disease, and depression. A key role in maintaining the balance between circadian rhythms and GM seems to be attributed to meal-timing and diet quality, as well as to certain microbial metabolites, in particular short-chain fatty acids.<br><br>CONCLUSIONS: Future studies are needed to decipher the link between the circadian rhythms and specific microbial patterns in relation to different disease frameworks.}, }
@article {pmid37245802, year = {2023}, author = {Toledo, S and Bondaruk, VF and Yahdjian, L and Oñatibia, GR and Loydi, A and Alberti, J and Bruschetti, M and Pascual, J and Peter, G and Agüero, WD and Namur, PR and Blanco, L and Peri, PL}, title = {Environmental factors regulate soil microbial attributes and their response to drought in rangeland ecosystems.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164406}, doi = {10.1016/j.scitotenv.2023.164406}, pmid = {37245802}, issn = {1879-1026}, abstract = {In ecosystems, soil microbial variables characterization are used to determine soil biological health and the response of soils to environmental stress. Although there are strong associations between plants and soil microorganisms, they may respond asynchronously to environmental factors and severe droughts. We aimed to: I) evaluate the special variation of soil microbiome such as microbial biomass carbon (MBC) and nitrogen (MBN), soil basal respiration (SBR) and microbial indexes in eight rangeland sites located across an aridity gradient (distributed from arid to mesic climates); II) analyze the relative importance of main environmental factors (climate, soils, and plants) and their relationships with microbial variables in the rangelands; and III) assess the effect of drought on microbial and plant variables in field-based manipulative experiments. First, we found significant changes of microbial variables along a precipitation and temperature gradient. The responses of MBC and MBN were strongly dependent on soil pH, soil nitrogen (N), soil organic carbon (SOC), C:N ratio and vegetation cover. In contrast, SBR was influenced by the aridity index (AI), the mean annual precipitation (MAP), the soil pH and vegetation cover. MBC, MBN and SBR were negatively related with soil pH compared to the other factors (C, N, C:N, vegetation cover, MAP and AI) that had a positive relationship. Second, we found a stronger soil microbial variables response to drought in arid sites compared to humid rangelands. Third, the responses of MBC, MBN, and SBR to drought showed positive relationships with vegetation cover and aboveground biomass, but with different regression slopes, this suggest that plant and microbial communities responded differently to drought. The results from this study improve our understanding about the microbial response to drought in different rangelands, and may facilitate the development of predictive models on responses of soil microorganisms in carbon cycle under global change scenarios.}, }
@article {pmid37245211, year = {2023}, author = {Alves, JC and Santos, A and Jorge, P and Pitães, &#xc2;}, title = {Faecal microbiome transplantation improves clinical signs of chronic idiopathic large bowel diarrhoea in working dogs.}, journal = {The Veterinary record}, volume = {}, number = {}, pages = {e3052}, doi = {10.1002/vetr.3052}, pmid = {37245211}, issn = {2042-7670}, abstract = {BACKGROUND: Chronic diarrhoea is a common clinical sign in dogs with chronic enteropathy, and psyllium husk has been shown to improve clinical signs in affected dogs. The aim of this study was to investigate whether faecal microbiome transplant has a similar effect in alleviating clinical signs in dogs with chronic large bowel diarrhoea.<br><br>METHOD: Thirty large-breed working dogs with chronic large bowel diarrhoea were divided into a psyllium group (PG) and a faecal microbiome transplant group (FMTG). To the PG, 16&#xa0;g/day of psyllium husk was administered for 30 days. The FMTG received faecal microbiome transplantation (FMT) once via enema. A daily log of faecal characteristics was kept, and the dogs' canine inflammatory bowel disease index (CIBDAI) and body condition scores (BCS) were determined. A Wilcoxon-Mann-Whitney test was used to compare group results. In addition, the Kaplan-Meier test was used to evaluate the occurrence rate of 1 day or more of diarrhoea and 2 days or more of diarrhoea by day 30.<br><br>RESULTS: The sample had a mean age of 3.9&#xa0;&#xb1;&#xa0;2.1 years and a bodyweight of 25.3&#xa0;&#xb1;&#xa0;6.8&#xa0;kg. The FMTG showed a more rapid onset of CIBDAI improvement but no difference in other measures. At 30 days, the FMTG showed a greater improvement in bodyweight and BCS, but no differences were observed in faecal scores, defaecation frequency and time of appearance of episodes of diarrhoea. Time played a significant positive role in the results observed across both groups (p < 0.05).<br><br>LIMITATIONS: This study did not compare the microbiomes of the dogs before and after treatment, so the role of specific types of bacteria cannot be determined.<br><br>CONCLUSION: Psyllium husk and FMT had similar effects in improving clinical signs of chronic large bowel diarrhoea.}, }
@article {pmid37245023, year = {2023}, author = {Becker, MF and Klueken, AM and Knief, C}, title = {Effects of above ground pathogen infection and fungicide application on the root-associated microbiota of apple saplings.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {43}, pmid = {37245023}, issn = {2524-6372}, abstract = {BACKGROUND: The root-associated microbiome has been of keen research interest especially in the last decade due to the large potential for increasing overall plant performance in agricultural systems. Knowledge about the impact of above ground plant disturbances on the root-associated microbiome remains limited. We addressed this by focusing on two potential impacts, foliar pathogen infection alone and in combination with the application of a plant health protecting product. We hypothesized that these lead to plant-mediated responses in the rhizosphere microbiota.<br><br>RESULTS: The effects of an infection of greenhouse grown apple saplings with either Venturia inaequalis or Podosphaera leucotricha as foliar pathogen, as well as the combined effect of P. leucotricha infection and foliar application of the synthetic plant health protecting product Aliette (active ingredient: fosetyl-aluminum), were studied on the root-associated microbiota. The bacterial community structure of rhizospheric soil and endospheric root material was characterized post-infection, using 16S rRNA gene amplicon sequencing. With increasing disease severity both pathogens led to changes in the rhizosphere and endosphere bacterial communities in comparison to uninfected plants (explained variance up to 17.7%). While the preventive application of Aliette on healthy plants two weeks prior inoculation did not induce changes in the root-associated microbiota, a second later application on the diseased plants decreased disease severity and resulted in differences of the rhizosphere bacterial community between infected and several of the cured plants, though differences were overall not statistically significant.<br><br>CONCLUSIONS: Foliar pathogen infections can induce plant-mediated changes in the root-associated microbiota, indicating that above ground disturbances are reflected in the below-ground microbiome, even though these become evident only upon severe leaf infection. The application of the fungicide Aliette on healthy plants itself did not induce any changes, but the application to diseased plants helped the plant to regain the microbiota of a healthy plant. These findings indicate that above ground agronomic management practices have implications for the root-associated microbiome, which should be considered in the context of microbiome management strategies.}, }
@article {pmid37244842, year = {2023}, author = {Thornton, CS and Magaret, AS and Carmody, LA and Kalikin, LM and Simon, RH and LiPuma, JJ and Caverly, LJ}, title = {Quantifying variation in home spirometry in people with cystic fibrosis during baseline health, and associations with clinical outcomes.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcf.2023.05.011}, pmid = {37244842}, issn = {1873-5010}, abstract = {BACKGROUND: Home spirometry is increasingly used to monitor lung function in people with cystic fibrosis (pwCF). Although decreases in lung function in the setting of increased respiratory symptoms are consistent with a pulmonary exacerbation (PEx), the interpretation of home spirometry during asymptomatic periods of baseline health is unclear. The aims of this study were to determine the variation in home spirometry in pwCF during asymptomatic periods of baseline health and to identify associations between this variation and PEx.<br><br>METHODS: Near-daily home spirometry measurements were obtained from a cohort of pwCF enrolled in a long-term study of the airway microbiome. Associations between the degree of variation in home spirometry and the time to next PEx were evaluated.<br><br>RESULTS: Thirteen subjects (mean age of 29 years and mean percent predicted forced expiratory volume in one second [ppFEV1] of 60) provided a median of 204 spirometry readings taken during 40 periods of baseline health. The mean week-to-week within-subject level of variation in ppFEV1 was 15.2&#xa0;&#xb1;&#xa0;6.2%. The degree of variation in ppFEV1 during baseline health was not associated with time to PEx.<br><br>CONCLUSIONS: Variation in ppFEV1 measured with near-daily home spirometry in pwCF during periods of baseline health exceeded the variation in ppFEV1 expected in clinic spirometry (based on ATS guidelines). The degree of variation in ppFEV1 during baseline health was not associated with time to PEx. These data are relevant for guiding interpretation of home spirometry.}, }
@article {pmid37244772, year = {2023}, author = {Eichner, M and Inomura, K and Pierella Karlusich, JJ and Shaked, Y}, title = {Better together? Lessons on sociality from Trichodesmium.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2023.05.001}, pmid = {37244772}, issn = {1878-4380}, abstract = {The N2-fixing cyanobacterium Trichodesmium is an important player in the oceanic nitrogen and carbon cycles. Trichodesmium occurs both as single trichomes and as colonies containing hundreds of trichomes. In this review, we explore the benefits and disadvantages of colony formation, considering physical, chemical, and biological effects from nanometer to kilometer scale. Showing that all major life challenges are affected by colony formation, we claim that Trichodesmium's ecological success is tightly linked to its colonial lifestyle. Microbial interactions in the microbiome, chemical gradients within the colony, interactions with particles, and elevated mobility in the water column shape a highly dynamic microenvironment. We postulate that these dynamics are key to the resilience of Trichodesmium and other colony formers in our changing environment.}, }
@article {pmid37244636, year = {2023}, author = {Hayward, SAL and Colinet, H}, title = {Metabolomics as a tool to elucidate biochemical cold adaptation in insects.}, journal = {Current opinion in insect science}, volume = {}, number = {}, pages = {101061}, doi = {10.1016/j.cois.2023.101061}, pmid = {37244636}, issn = {2214-5753}, abstract = {Metabolomics is an incredibly valuable tool in helping understand insect responses to cold. It not only characterizes how low temperature disrupts metabolic homeostasis, but also how it triggers fundamental adaptive responses, e.g. homeoviscous adaptation and cryoprotectant accumulation. This review outlines the advantages and disadvantages of different metabolomic technologies (NMR- vs. MS-based) and screening approaches (targeted vs. untargeted). We emphasize the importance of time series and tissue-specific data, as well as the challenges of disentangling insect vs. microbiome responses. In addition, we set out the need to move beyond simple correlations between metabolite abundance and tolerance phenotypes by undertaking functional assessments, e.g. using dietary supplementation or injections. We highlight studies at the vanguard of employing these approaches, and where key knowledge gaps remain.}, }
@article {pmid37244494, year = {2023}, author = {Daghighi, E and Shah, T and Wainkwa Chia, R and Lee, JY and Shang, J and Rodríguez-Seijo, A}, title = {The forgotten impacts of plastic contamination on terrestrial micro- and mesofauna: A call for research.}, journal = {Environmental research}, volume = {}, number = {}, pages = {116227}, doi = {10.1016/j.envres.2023.116227}, pmid = {37244494}, issn = {1096-0953}, abstract = {Microplastics (MP) and nanoplastics (NP) contamination of the terrestrial environment is a growing concern worldwide and is thought to impact soil biota, particularly the micro and mesofauna community, by various processes that may contribute to global change in terrestrial systems. Soils act as a long-term sink for MP, accumulating these contaminants and increasing their adverse impacts on soil ecosystems. Consequently, the whole terrestrial ecosystem is impacted by microplastic pollution, which also threatens human health by their potential transfer to the soil food web. In general, the ingestion of MP in different concentrations by soil micro and mesofauna can adversely affect their development and reproduction, impacting terrestrial ecosystems. MP in soil moves horizontally and vertically because of the movement of soil organisms and the disturbance caused by plants. However, the effects of MP on terrestrial micro-and mesofauna are largely overlooked. Here, we give the most recent information on the forgotten impacts of MP contamination of soil on microfauna and mesofauna communities (protists, tardigrades, soil rotifers, nematodes, collembola and mites). More than 50 studies focused on the impact of MP on these organisms between 1990 and 2022 have been reviewed. In general, plastic pollution does not directly affect the survival of organisms, except under co-contaminated plastics that can increase adverse effects (e.g. tire-tread particles on springtails). Besides, they can have adverse effects at oxidative stress and reduced reproduction (protists, nematodes, potworms, springtails or mites). It was observed that micro and mesofauna could act as passive plastic transporters, as shown for springtails or mites. Finally, this review discusses how soil micro- and mesofauna play a key role in facilitating the (bio-)degradation and movement of MP and NP through soil systems and, therefore, the potential transfer to soil depths. More research should be focused on plastic mixtures, community level and long-term experiments.}, }
@article {pmid37244405, year = {2023}, author = {Eltay, EG and Van Dyke, T}, title = {Resolution of inflammation in oral diseases.}, journal = {Pharmacology &amp; therapeutics}, volume = {}, number = {}, pages = {108453}, doi = {10.1016/j.pharmthera.2023.108453}, pmid = {37244405}, issn = {1879-016X}, abstract = {The resolution of inflammation is an essential endogenous process that protects host tissues from an exaggerated chronic inflammatory response. Multiple interactions between host cells and resident oral microbiome regulate the protective functions that lead to inflammation in the oral cavity. Failure of appropriate regulation of inflammation can lead to chronic inflammatory diseases that result from an imbalance between pro-inflammatory and pro-resolution mediators. Thus, failure of the host to resolve inflammation can be considered an essential pathological mechanism for progression from the late stages of acute inflammation to a chronic inflammatory response. Specialized pro-resolving mediators (SPMs), which are essential polyunsaturated fatty acid (PUFA)-derived autacoid mediators, aid in regulating the endogenous inflammation resolving process by stimulating immune cell-mediated clearance of apoptotic polymorphonuclear neutrophils, cellular debris, and microbes, restricting further neutrophil tissue infiltration, and counter-regulating pro-inflammatory cytokine production. The SPM superfamily contains four specialized lipid mediator families: lipoxins, resolvins, protectins, and maresins that can activate resolution pathways. Understanding the crosstalk between resolution signals in the tissue response to injury has therapeutic application potential for preventing, maintaining, and regenerating chronically damaged tissues. Here, we discuss the fundamental concepts of resolution as an active biochemical process, novel concepts demonstrating the role of resolution mediators in tissue regeneration in periodontal and pulpal diseases, and future directions for therapeutic applications with particular emphasis on periodontal therapy.}, }
@article {pmid37244386, year = {2023}, author = {Zhang, Y and Chen, T and Hao, X and Hu, Y and Chen, M and Zhang, D and Cai, H and Luo, J and Kong, L and Huang, S and Huang, Y and Yang, N and Liu, R and Li, Q and Yuan, C and Wang, C and Zhou, H and Huang, W and Zhang, W}, title = {Mapping the regulatory effects of herbal organic compounds on gut bacteria.}, journal = {Pharmacological research}, volume = {193}, number = {}, pages = {106804}, doi = {10.1016/j.phrs.2023.106804}, pmid = {37244386}, issn = {1096-1186}, abstract = {Herbal organic compounds (HOCs) are bioactive natural products from medicinal plants and some traditional Chinese medicines (TCMs). Recently, ingestion of a few HOCs with low bioavailability has been associated with alterations in gut microbiota, but the extent of this phenomenon remains unclear. Here, we systematically screened 481 HOCs against 47 representative gut bacterial strains in vitro and found that almost one-third of the HOCs exhibited unique anticommensal activity. Quinones showed a potent anticommensal activity, while saturated fatty acids exhibited stronger inhibition of the Lactobacillus genus. Flavonoids, phenylpropanoids, terpenoids, triterpenoids, alkaloids and phenols displayed weaker anticommensal activity, but steroids, saccharides and glycosides had hardly any effect on strain growth. Notably, S-configuration HOCs demonstrated stronger anticommensal activity than R-configuration HOCs. The strict screening conditions ensured high accuracy (95%) through benchmarking validation. Additionally, the effects of HOCs on human fecal microbiota profiling were positively correlated with their anticommensal activity against bacterial strains. Molecular and chemical features such as AATS3i and XLogP3 were correlated with the anticommensal activity of the HOCs in the random forest classifier. Finally, we validated that curcumin, a polyhydric phenol with anticommensal activity, improved insulin resistance in HFD mice by modulating the composition and metabolic function of gut microbiota. Our results systematically mapped the profile of HOCs directly affecting human gut bacterial strains, offering a resource for future research on HOC-microbiota interaction, and broadening our understanding of natural product utilization through gut microbiota modulation.}, }
@article {pmid37244016, year = {2023}, author = {Lee, MH and Choi, SJ and Jang, D and Kang, S and Jung, HJ and Hwang, DS}, title = {A peptide of PilZ domain-containing protein controls wastewater-treatment-membrane biofouling by inducing bacterial attachment.}, journal = {Water research}, volume = {240}, number = {}, pages = {120085}, doi = {10.1016/j.watres.2023.120085}, pmid = {37244016}, issn = {1879-2448}, abstract = {Membrane-based wastewater reclamation is used to mitigate water scarcity; however, irreversible biofouling is an elusive problem that hinders the efficiency of a forward-osmosis (FO) membrane-based process, and the protein responsible for fouling is unknown. Herein, we identified fouling proteins by analyzing the microbiome and proteome of wastewater extracellular polymeric substances responsible for strong irreversible FO-membrane fouling. The IGLSSLPR peptide of a PilZ domain-containing protein was found to recruit bacterial attachment when immobilized on the membrane surface while suppressing it when dissolved, in a similar manner to the Arg-Gly-Asp (RGD) peptide in mammalian cell cultures. Bacteria adhere to IGLSSLPR and poly-l-lysine-coated membranes with similar energies and exhibit water fluxes that decline similarly, which is ascribable to interaction as strong as electrostatic interactions in the peptide-coated membranes. We conclude that IGLSSLPR is the key domain responsible for membrane fouling and can be used to develop antifouling technology against bacteria, which is similar to the current usage of RGD peptide in mammalian cell cultures.}, }
@article {pmid37244006, year = {2023}, author = {Sun, NY and Chen, S and Li, Y}, title = {Lactobacillus paracasei L9 ameliorated obesity-associated metabolic parameters and relevant gut microbiota in mice fed a high-fat diet.}, journal = {Nutrition research (New York, N.Y.)}, volume = {115}, number = {}, pages = {26-37}, doi = {10.1016/j.nutres.2023.04.003}, pmid = {37244006}, issn = {1879-0739}, abstract = {The purpose of the present study was to determine whether Lactobacillus paracasei L9 (L9) supplementation prevents diet-induced obesity in C57BL/6J mice. Four-week-old mice were fed a high-fat diet (HFD) for 12 weeks and then supplemented with or without L9 for another 12 weeks. Weight gain, white adipose tissue weight, plasma lipid levels of total cholesterol, triglyceride, and low-density lipoprotein-cholesterol were significantly increased in the HFD group compared with those in the control group and were decreased by L9 treatment. The fat deposits in the liver and epididymal adipose tissue were increased in the HFD group compared with the normal chow diet group and decreased by L9 treatment. Reverse transcriptase-polymerase chain reaction analyses revealed that L9 suppressed pro-inflammatory cytokine and lipid synthesis-related genes in epididymal adipose tissue. This study used Illumina Miseq sequencing to explore alterations of the gut microbiome. L9 ameliorated HFD-induced structural dysbiosis and gut bacteria that were positively related with obesity phenotypes were obviously decreased. Altogether, the findings indicate that administration of L9 ameliorates HFD-induced hyperlipidemia and lipid accumulation in liver and inflammation associated with intestinal dysbiosis in obese mice. These findings suggest that L9 supplementation may provide a natural alternative to attenuate obesity.}, }
@article {pmid37243047, year = {2023}, author = {Shen, Y and Dong, Y and Jiao, J and Wang, P and Chen, M and Li, J}, title = {BBIBP-CorV Vaccination against the SARS-CoV-2 Virus Affects the Gut Microbiome.}, journal = {Vaccines}, volume = {11}, number = {5}, pages = {}, pmid = {37243047}, issn = {2076-393X}, abstract = {Several observational studies have confirmed that the severe acute respiratory syndrome coronavirus2 (SARS-CoV-2) might substantially affect the gastrointestinal (GI) system by replicating in human small intestine enterocytes. Yet, so far, no study has reported the effects of inactivated SARS-CoV-2 virus vaccines on gut microbiota alterations. In this study, we examined the effects of the BBIBP-CorV vaccine (ChiCTR2000032459, sponsored by the Beijing Institute of Biological Products/Sinopharm), on gut microbiota. Fecal samples were collected from individuals whoreceived two doses of intramuscular injection of BBIBP-CorV and matched unvaccinated controls. DNA extracted from fecal samples was subjected to 16S ribosomal RNA sequencing analysis. The composition and biological functions of the microbiota between vaccinated and unvaccinated individuals were compared. Compared with unvaccinated controls, vaccinated subjects exhibited significantly reduced bacterial diversity, elevated firmicutes/bacteroidetes (F/B) ratios, a tendency towards Faecalibacterium-predominant enterotypes, and altered gut microbial compositions and functional potentials. Specifically, the intestinal microbiota in vaccine recipients was enriched with Faecalibacterium and Mollicutes and with a lower abundance of Prevotella, Enterococcus, Leuconostocaceae, and Weissella. Microbial function prediction by phylogenetic investigation of communities using reconstruction of unobserved states (PICRUSt) analysis further indicated that Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways involved in carbohydrate metabolism and transcription were positively associated with vaccine inoculation, whereas capacities in neurodegenerative diseases, cardiovascular diseases, and cancers were negatively affected by vaccines. Vaccine inoculation was particularly associated with gut microbiota alterations, as was demonstrated by the improved composition and functional capacities of gut microbiota.}, }
@article {pmid37242791, year = {2023}, author = {Jati, S and Mahata, S and Das, S and Chatterjee, S and Mahata, SK}, title = {Catestatin: Antimicrobial Functions and Potential Therapeutics.}, journal = {Pharmaceutics}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/pharmaceutics15051550}, pmid = {37242791}, issn = {1999-4923}, support = {1 R21 AG072487-01 and 1 R21 AG080246-01 to S.K.M./NH/NIH HHS/United States ; }, abstract = {The rapid increase in drug-resistant and multidrug-resistant infections poses a serious challenge to antimicrobial therapies, and has created a global health crisis. Since antimicrobial peptides (AMPs) have escaped bacterial resistance throughout evolution, AMPs are a category of potential alternatives for antibiotic-resistant "superbugs". The Chromogranin A (CgA)-derived peptide Catestatin (CST: hCgA352-372; bCgA344-364) was initially identified in 1997 as an acute nicotinic-cholinergic antagonist. Subsequently, CST was established as a pleiotropic hormone. In 2005, it was reported that N-terminal 15 amino acids of bovine CST (bCST1-15 aka cateslytin) exert antibacterial, antifungal, and antiyeast effects without showing any hemolytic effects. In 2017, D-bCST1-15 (where L-amino acids were changed to D-amino acids) was shown to exert very effective antimicrobial effects against various bacterial strains. Beyond antimicrobial effects, D-bCST1-15 potentiated (additive/synergistic) antibacterial effects of cefotaxime, amoxicillin, and methicillin. Furthermore, D-bCST1-15 neither triggered bacterial resistance nor elicited cytokine release. The present review will highlight the antimicrobial effects of CST, bCST1-15 (aka cateslytin), D-bCST1-15, and human variants of CST (Gly364Ser-CST and Pro370Leu-CST); evolutionary conservation of CST in mammals; and their potential as a therapy for antibiotic-resistant "superbugs".}, }
@article {pmid37242596, year = {2023}, author = {Ahmed, AA and Otten, AT and Gareb, B and Huijmans, JE and Eissens, AC and Rehman, A and Dijkstra, G and Kosterink, JGW and Frijlink, HW and Schellekens, RCA}, title = {Capsules with Ileocolonic-Targeted Release of Vitamin B2, B3, and C (ColoVit) Intended for Optimization of Gut Health: Development and Validation of the Production Process.}, journal = {Pharmaceutics}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/pharmaceutics15051354}, pmid = {37242596}, issn = {1999-4923}, abstract = {The ileocolonic-targeted delivery of vitamins can establish beneficial alterations in gut microbial composition. Here, we describe the development of capsules containing riboflavin, nicotinic acid, and ascorbic acid covered with a pH-sensitive coating (ColoVit) to establish site-specific release in the ileocolon. Ingredient properties (particle size distribution, morphology) relevant for formulation and product quality were determined. Capsule content and the in vitro release behaviour were determined using a HPLC-method. Uncoated and coated validation batches were produced. Release characteristics were evaluated using a gastro-intestinal simulation system. All capsules met the required specifications. The contents of the ingredients were in the 90.0-120.0% range, and uniformity requirements were met. In the dissolution test a lag-time in drug release of 277-283 min was found, which meets requirements for ileocolonic release. The release itself is immediate as shown by dissolution of the vitamins of more than 75% in 1 h. The production process of the ColoVit formulation was validated and reproducible, it was shown that the vitamin blend was stable during the production process and in the finished coated product. The ColoVit is intended as an innovative treatment approach for beneficial microbiome modulation and optimization of gut health.}, }
@article {pmid37242497, year = {2023}, author = {Filidou, E and Kolios, G}, title = {Special Issue "Gut Microbiota, Inflammatory Bowel Diseases, and Therapeutic Targets".}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/ph16050714}, pmid = {37242497}, issn = {1424-8247}, abstract = {The gut microbiota and its overall genetic composition, the microbiome, have been the subject of extensive research over the last decade within the fields of genomics, transcriptomics and metabolomics, and their role in various other targeted approaches and advanced technologies has been explored [...].}, }
@article {pmid37242478, year = {2023}, author = {Chaiyasut, C and Sivamaruthi, BS and Lailerd, N and Sirilun, S and Thangaleela, S and Khongtan, S and Bharathi, M and Kesika, P and Saelee, M and Choeisoongnern, T and Fukngoen, P and Peerajan, S and Sittiprapaporn, P}, title = {Influence of Bifidobacterium breve on the Glycaemic Control, Lipid Profile and Microbiome of Type 2 Diabetic Subjects: A Preliminary Randomized Clinical Trial.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/ph16050695}, pmid = {37242478}, issn = {1424-8247}, abstract = {Type 2 diabetes mellitus (T2DM) is one of the most highly prevalent metabolic disorders worldwide. Uncontrolled T2DM can lead to other health threats such as cardiac arrest, lower-limb amputation, blindness, stroke, impaired kidney function, and microvascular and macrovascular complications. Many studies have demonstrated the association between gut microbiota and diabetes development and probiotic supplementation in improving glycemic properties in T2DM. The study aimed to evaluate the influence of Bifidobacterium breve supplementation on glycemic control, lipid profile, and microbiome of T2DM subjects. Forty participants were randomly divided into two groups, and they received probiotics (50 × 10[9] CFU/day) or placebo interventions (corn starch; 10 mg/day) for 12 weeks. The changes in the blood-urea nitrogen (BUN), aspartate aminotransferase (AST), alanine transaminase (ALT), alkaline phosphatase (ALP), fasting blood sugar (FBS), glycated hemoglobin (HbA1c), total cholesterol (TC), triglycerides (TG), high-density lipoprotein (HDL), low-density lipoprotein (LDL), creatinine levels, and other factors such as body-mass index, visceral fat, body fat, and body weight were assessed at baseline and after 12 weeks. B. breve supplementation significantly reduced BUN, creatinine, LDL, TG, and HbA1c levels compared to the placebo group. Significant changes were observed in the microbiome of the probiotic-treated group compared to the placebo group. Firmicutes and proteobacteria were predominant in the placebo and probiotic-treated groups. Genera Streptococcus, Butyricicoccus, and species Eubacterium hallii were significantly reduced in the probiotic-treated group compared to the placebo. Overall results suggested that B. breve supplementation could prevent worsening of representative clinical parameters in T2DM subjects. The current study has limitations, including fewer subjects, a single probiotic strain, and fewer metagenomic samples for microbiome analysis. Therefore, the results of the current study require further validation using more experimental subjects.}, }
@article {pmid37242469, year = {2023}, author = {Ivanova, AY and Shirokov, IV and Toshchakov, SV and Kozlova, AD and Obolenskaya, ON and Mariasina, SS and Ivlev, VA and Gartseev, IB and Medvedev, OS}, title = {Effects of Coenzyme Q10 on the Biomarkers (Hydrogen, Methane, SCFA and TMA) and Composition of the Gut Microbiome in Rats.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/ph16050686}, pmid = {37242469}, issn = {1424-8247}, abstract = {The predominant route of administration of drugs with coenzyme Q10 (CoQ10) is administration per os. The bioavailability of CoQ10 is about 2-3%. Prolonged use of CoQ10 to achieve pharmacological effects contributes to the creation of elevated concentrations of CoQ10 in the intestinal lumen. CoQ10 can have an effect on the gut microbiota and the levels of biomarkers it produces. CoQ10 at a dose of 30 mg/kg/day was administered per os to Wistar rats for 21 days. The levels of gut microbiota biomarkers (hydrogen, methane, short-chain fatty acids (SCFA), and trimethylamine (TMA)) and taxonomic composition were measured twice: before the administration of CoQ10 and at the end of the experiment. Hydrogen and methane levels were measured using the fasting lactulose breath test, fecal and blood SCFA and fecal TMA concentrations were determined by NMR, and 16S sequencing was used to analyze the taxonomic composition. Administration of CoQ10 for 21 days resulted in a 1.83-fold (p = 0.02) increase in hydrogen concentration in the total air sample (exhaled air + flatus), a 63% (p = 0.02) increase in the total concentration of SCFA (acetate, propionate, butyrate) in feces, a 126% increase in butyrate (p = 0.04), a 6.56-fold (p = 0.03) decrease in TMA levels, a 2.4-fold increase in relative abundance of Ruminococcus and Lachnospiraceae AC 2044 group by 7.5 times and a 2.8-fold decrease in relative representation of Helicobacter. The mechanism of antioxidant effect of orally administered CoQ10 can include modification of the taxonomic composition of the gut microbiota and increased generation of molecular hydrogen, which is antioxidant by itself. The evoked increase in the level of butyric acid can be followed by protection of the gut barrier function.}, }
@article {pmid37242437, year = {2023}, author = {Minervini, G and Franco, R and Marrapodi, MM and Fiorillo, L and Badnjević, A and Cervino, G and Cicciù, M}, title = {Probiotics in the Treatment of Radiotherapy-Induced Oral Mucositis: Systematic Review with Meta-Analysis.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/ph16050654}, pmid = {37242437}, issn = {1424-8247}, abstract = {The inflammatory injury of the mucous membranes lining the digestive tract, from the mouth to the anus, is called mucositis. One of the intriguing and compelling new therapeutic modalities that has emerged in recent decades due to advances in our understanding of this condition's pathophysiology is probiotics. The purpose of this meta-analysis is to evaluate the efficiency of probiotics in the treatment of chemotherapy-induced mucositis for head and neck malignancies; a literature search was performed on PubMed, Lilacs, and Web of Science, and articles published from 2000 to 31 January 2023 were considered, according to the keywords entered. The term "Probiotics" was combined with "oral mucositis" using the Boolean connector AND; at the end of the research, 189 studies were identified from the search on the three engines. Only three were used to draw up the present systematic study and metanalysis; this meta-analysis showed that the treatment of mucositis with probiotics is an effective method, and the analysis of the results of these studies showed that the use of probiotics promoted a decrease in the severity of mucositis symptoms.}, }
@article {pmid37242433, year = {2023}, author = {Cesar, T and Salgaço, MK and Mesa, V and Sartoratto, A and Sivieri, K}, title = {Exploring the Association between Citrus Nutraceutical Eriocitrin and Metformin for Improving Pre-Diabetes in a Dynamic Microbiome Model.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/ph16050650}, pmid = {37242433}, issn = {1424-8247}, abstract = {Pre-diabetes is recognized as an altered metabolic state, which precedes type 2 diabetes, and it is associated with great dysfunction of the intestinal microbiota, known as dysbiosis. Natural compounds, capable of reducing blood glucose without side effects and with a beneficial effect on the microbiota, have been studied as substitutes or adjuvants to conventional hypoglycemic agents, such as metformin. In this work, the effect of the nutraceutical Eriomin[®], a mixture of citrus flavonoids (eriocitrin, hesperidin, naringin, and didymin), which reduces glycemia and increases glucagon-like peptide-1 (GLP-1) in pre-diabetic patients, was tested in the Simulator of Human Intestinal Microbial Ecosystem (SHIME[®]), inoculated with pre-diabetic microbiota. After treatment with Eriomin[®] plus metformin, a significant increase in acetate and butyrate production was observed. Furthermore, sequencing of the 16S rRNA gene of the microorganisms showed that Eriomin[®] plus metformin stimulated the growth of Bacteroides and Subdoligranulum genera. Bacteroides are the largest fraction of the intestinal microbiota and are potential colonizers of the colon, with some species producing acetic and propionic fatty acids. In addition, Subdoligranulum species are associated with better host glycemic metabolism. In conclusion, Eriomin[®] associated with metformin improved the composition and metabolism of the intestinal microbiota, suggesting a potential use in pre-diabetes therapy.}, }
@article {pmid37242408, year = {2023}, author = {Fowler, EC and Samuel, RS and St-Pierre, B}, title = {A Comparative Analysis of the Fecal Bacterial Communities of Light and Heavy Finishing Barrows Raised in a Commercial Swine Production Environment.}, journal = {Pathogens (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, doi = {10.3390/pathogens12050738}, pmid = {37242408}, issn = {2076-0817}, abstract = {For commercial swine producers, the natural variation in body weight amongst pigs in a herd presents a challenge in meeting the standards of meat processors who incentivize target carcass weights by offering more favorable purchase prices. Body weight variation in a swine herd is evident as early as birth, and it is typically maintained throughout the entire production cycle. Amongst the various factors that can affect growth performance, the gut microbiome has emerged as an important factor that can affect efficiency, as it contributes to vital functions such as providing assimilable nutrients from feed ingredients that are inedible to the host, as well as resistance to infection by a pathogen. In this context, the objective of the study described in this report was to compare the fecal microbiomes of light and heavy barrows (castrated male finishing pigs) that were part of the same research herd that was raised under commercial conditions. Using high-throughput sequencing of amplicons generated from the V1-V3 regions of the 16S rRNA gene, two abundant candidate bacterial species identified as operational taxonomic units (OTUs), Ssd-1085 and Ssd-1144, were found to be in higher abundance in the light barrows group. Ssd-1085 was predicted to be a potential strain of Clostridium jeddahitimonense, a bacterial species capable of utilizing tagatose, a monosaccharide known to act as a prebiotic that can enhance the proliferation of beneficial microorganisms while inhibiting the growth of bacterial pathogens. OTU Ssd-1144 was identified as a candidate strain of C. beijerinckii, which would be expected to function as a starch utilizing symbiont in the swine gut. While it remains to be determined why putative strains of these beneficial bacterial species would be in higher abundance in lower weight pigs, their overall high levels in finishing pigs could be the result of including ingredients such as corn and soybean-based products in swine diets. Another contribution from this study was the determination that these two OTUs, along with five others that were also abundant in the fecal bacterial communities of the barrows that were analyzed, had been previously identified in weaned pigs, suggesting that these OTUs can become established as early as the nursery phase.}, }
@article {pmid37242367, year = {2023}, author = {Chen, Y and Song, Y and Chen, Z and Yau, JWK and Chan, KCC and Leung, ASY and Chan, OM and Yeung, ACM and Yuen, CLY and Chan, PKS and Tam, WH and Leung, TF}, title = {Early-Life Skin Microbial Biomarkers for Eczema Phenotypes in Chinese Toddlers.}, journal = {Pathogens (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, doi = {10.3390/pathogens12050697}, pmid = {37242367}, issn = {2076-0817}, abstract = {Eczema is a common inflammatory skin disorder during infancy. Evidence has shown that skin-microbiome fluctuations may precede eczema development, but their predictive value for eczema phenotypes remains unknown. We aimed to investigate the early-life evolution of the skin microbiome and its temporal associations with different pairs of eczema phenotypes (transient versus persistent, atopic versus non-atopic) in Chinese children. We followed 119 term Chinese infants from birth to 24 months old within a Hong Kong birth cohort. The skin microbes at the left antecubital fossa were serially sampled by flocked swabs at 1, 6, and 12 months for bacterial 16S rRNA gene sequencing. The atopic sensitization at 12 months was strongly associated with eczema persisting to 24 months (odds ratio 4.95, 95% confidence interval 1.29-19.01). Compared with those with non-atopic eczema, the children with atopic eczema had reduced alpha diversity at 12 months (p < 0.001) and transiently higher abundance of the genus Janibacter at 6 months (p < 0.001). Our findings suggest that atopic sensitization at 12 months may predict persistent eczema by 24 months, and atopic eczema at 12 months is associated with unique skin microbiome profiles at 6 and 12 months. Non-invasive skin-microbiome profiling may have predictive value for atopic eczema.}, }
@article {pmid37242309, year = {2023}, author = {Samuelson, DR and Smith, DR and Cunningham, KC and Haq, S and Villageliú, DN and Ellis, CM and Chowdhury, NB and Ramer-Tait, AE and Price, JD and Knoell, DL}, title = {The Inherited Intestinal Microbiota from Myeloid-Specific ZIP8KO Mice Impairs Pulmonary Host Defense against Pneumococcal Pneumonia.}, journal = {Pathogens (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, doi = {10.3390/pathogens12050639}, pmid = {37242309}, issn = {2076-0817}, support = {R01-HL156952/NH/NIH HHS/United States ; R00-AA026336/NH/NIH HHS/United States ; R01-DK131990-01/NH/NIH HHS/United States ; }, abstract = {Intestinal dysbiosis increases susceptibility to infection through the alteration of metabolic profiles, which increases morbidity. Zinc (Zn) homeostasis in mammals is tightly regulated by 24 Zn transporters. ZIP8 is unique in that it is required by myeloid cells to maintain proper host defense against bacterial pneumonia. In addition, a frequently occurring ZIP8 defective variant (SLC39A8 rs13107325) is strongly associated with inflammation-based disorders and bacterial infection. In this study, we developed a novel model to study the effects of ZIP8-mediated intestinal dysbiosis on pulmonary host defense independent of the genetic effects. Cecal microbial communities from a myeloid-specific Zip8 knockout mouse model were transplanted into germ-free mice. Conventionalized ZIP8KO-microbiota mice were then bred to produce F1 and F2 generations of ZIP8KO-microbiota mice. F1 ZIP8KO-microbiota mice were also infected with S. pneumoniae, and pulmonary host defense was assessed. Strikingly, the instillation of pneumococcus into the lung of F1 ZIP8KO-microbiota mice resulted in a significant increase in weight loss, inflammation, and mortality when compared to F1 wild-type (WT)-microbiota recipients. Similar defects in pulmonary host defense were observed in both genders, although consistently greater in females. From these results, we conclude that myeloid Zn homeostasis is not only critical for myeloid function but also plays a significant role in the maintenance and control of gut microbiota composition. Further, these data demonstrate that the intestinal microbiota, independent of host genetics, play a critical role in governing host defense in the lung against infection. Finally, these data strongly support future microbiome-based interventional studies, given the high incidence of zinc deficiency and the rs13107325 allele in humans.}, }
@article {pmid37242222, year = {2023}, author = {Hill, DR and Buck, RH}, title = {Infants Fed Breastmilk or 2'-FL Supplemented Formula Have Similar Systemic Levels of Microbiota-Derived Secondary Bile Acids.}, journal = {Nutrients}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/nu15102339}, pmid = {37242222}, issn = {2072-6643}, abstract = {Human milk represents an optimal source of nutrition during infancy. Milk also serves as a vehicle for the transfer of growth factors, commensal microbes, and prebiotic compounds to the immature gastrointestinal tract. These immunomodulatory and prebiotic functions of milk are increasingly appreciated as critical factors in the development of the infant gut and its associated microbial community. Advances in infant formula composition have sought to recapitulate some of the prebiotic and immunomodulatory functions of milk through human milk oligosaccharide (HMO) fortification, with the aim of promoting healthy development both within the gastrointestinal tract and systemically. Our objective was to investigate the effects of feeding formulas supplemented with the HMO 2'-fucosyllactose (2'-FL) on serum metabolite levels relative to breastfed infants. A prospective, randomized, double-blinded, controlled study of infant formulas (64.3 kcal/dL) fortified with varying levels of 2'-FL and galactooligosaccharides (GOS) was conducted [0.2 g/L 2'-FL + 2.2 g/L GOS; 1.0 g/L 2'-FL + 1.4 g/L GOS]. Healthy singleton infants age 0-5 days and with birth weight > 2490 g were enrolled (n = 201). Mothers chose to either exclusively formula-feed or breastfeed their infant from birth to 4 months of age. Blood samples were drawn from a subset of infants at 6 weeks of age (n = 35-40 per group). Plasma was evaluated by global metabolic profiling and compared to a breastfed reference group (HM) and a control formula (2.4 g/L GOS). Fortification of control infant formula with the HMO 2'-FL resulted in significant increases in serum metabolites derived from microbial activity in the gastrointestinal tract. Most notably, secondary bile acid production was broadly increased in a dose-dependent manner among infants receiving 2'-FL supplemented formula relative to the control formula. 2'-FL supplementation increased secondary bile acid production to levels associated with breastfeeding. Our data indicate that supplementation of infant formula with 2'-FL supports the production of secondary microbial metabolites at levels comparable to breastfed infants. Thus, dietary supplementation of HMO may have broad implications for the function of the gut microbiome in systemic metabolism. This trial was registered at with the U.S. National library of Medicine as NCT01808105.}, }
@article {pmid37242207, year = {2023}, author = {Tan, KML and Chee, J and Lim, KLM and Ng, M and Gong, M and Xu, J and Tin, F and Natarajan, P and Lee, BL and Ong, CN and Tint, MT and Kee, MZL and Müller-Riemenschneider, F and Gluckman, PD and Meaney, MJ and Kumar, M and Karnani, N and Eriksson, JG and Nandanan, B and Wyss, A and Cameron-Smith, D}, title = {Safety, Tolerability, and Pharmacokinetics of β-Cryptoxanthin Supplementation in Healthy Women: A Double-Blind, Randomized, Placebo-Controlled Clinical Trial.}, journal = {Nutrients}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/nu15102325}, pmid = {37242207}, issn = {2072-6643}, abstract = {BACKGROUND: β-cryptoxanthin is a dietary carotenoid for which there have been few studies on the safety and pharmacokinetics following daily oral supplementation.<br><br>METHODS: 90 healthy Asian women between 21 and 35 years were randomized into three groups: 3 and 6 mg/day oral &#x3b2;-cryptoxanthin, and placebo. At 2, 4, and 8 weeks of supplementation, plasma carotenoid levels were measured. The effects of &#x3b2;-cryptoxanthin on blood retinoid-dependent gene expression, mood, physical activity and sleep, metabolic parameters, and fecal microbial composition were investigated.<br><br>RESULTS: &#x3b2;-cryptoxanthin supplementation for 8 weeks (3 and 6 mg/day) was found to be safe and well tolerated. Plasma &#x3b2;-cryptoxanthin concentration was significantly higher in the 6 mg/day group (9.0 &#xb1; 4.1 &#xb5;mol/L) compared to 3 mg/day group (6.0 &#xb1; 2.6 &#xb5;mol/L) (p < 0.03), and placebo (0.4 &#xb1; 0.1 &#xb5;mol/L) (p < 0.001) after 8 weeks. Plasma all-trans retinol, &#x3b1;-cryptoxanthin, &#x3b1;-carotene, &#x3b2;-carotene, lycopene, lutein, and zeaxanthin levels were not significantly changed. No effects were found on blood retinol-dependent gene expression, mood, physical activity and sleep, metabolic parameters, and fecal microbial composition.<br><br>CONCLUSIONS: Oral &#x3b2;-cryptoxanthin supplementation over 8 weeks lead to high plasma concentrations of &#x3b2;-cryptoxanthin, with no impact on other carotenoids, and was well tolerated in healthy women.}, }
@article {pmid37242119, year = {2023}, author = {Puljiz, Z and Kumric, M and Vrdoljak, J and Martinovic, D and Ticinovic Kurir, T and Krnic, MO and Urlic, H and Puljiz, Z and Zucko, J and Dumanic, P and Mikolasevic, I and Bozic, J}, title = {Obesity, Gut Microbiota, and Metabolome: From Pathophysiology to Nutritional Interventions.}, journal = {Nutrients}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/nu15102236}, pmid = {37242119}, issn = {2072-6643}, abstract = {Obesity is a disorder identified by an inappropriate increase in weight in relation to height and is considered by many international health institutions to be a major pandemic of the 21st century. The gut microbial ecosystem impacts obesity in multiple ways that yield downstream metabolic consequences, such as affecting systemic inflammation, immune response, and energy harvest, but also the gut-host interface. Metabolomics, a systematized study of low-molecular-weight molecules that take part in metabolic pathways, represents a serviceable method for elucidation of the crosstalk between hosts' metabolism and gut microbiota. In the present review, we confer about clinical and preclinical studies exploring the association of obesity and related metabolic disorders with various gut microbiome profiles, and the effects of several dietary interventions on gut microbiome composition and the metabolome. It is well established that various nutritional interventions may serve as an efficient therapeutic approach to support weight loss in obese individuals, yet no agreement exists in regard to the most effective dietary protocol, both in the short and long term. However, metabolite profiling and the gut microbiota composition might represent an opportunity to methodically establish predictors for obesity control that are relatively simple to measure in comparison to traditional approaches, and it may also present a tool to determine the optimal nutritional intervention to ameliorate obesity in an individual. Nevertheless, a lack of adequately powered randomized trials impedes the application of observations to clinical practice.}, }
@article {pmid37240974, year = {2023}, author = {Karakasidis, E and Kotsiou, OS and Gourgoulianis, KI}, title = {Lung and Gut Microbiome in COPD.}, journal = {Journal of personalized medicine}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/jpm13050804}, pmid = {37240974}, issn = {2075-4426}, abstract = {Chronic obstructive pulmonary disease (COPD) is one of the leading causes of death worldwide. The association between lung and gut microbiomes in the pathogenesis of COPD has been recently uncovered. The goal of this study was to discuss the role of the lung and gut microbiomes in COPD pathophysiology. A systematic search of the PubMed database for relevant articles submitted up to June 2022 was performed. We examined the association between the lung and gut microbiome dysbiosis, reflected in bronchoalveolar lavage (BAL), lung tissue, sputum, and feces samples, and the pathogenesis and progression of COPD. It is evident that the lung and gut microbiomes affect each other and both play a vital role in the pathogenesis of COPD. However, more research needs to be carried out to find the exact associations between microbiome diversity and COPD pathophysiology and exacerbation genesis. Another field that research should focus on is the impact of treatment interventions targeting the human microbiome in preventing COPD genesis and progression.}, }
@article {pmid37240844, year = {2023}, author = {Javan Balegh Marand, A and Baars, C and Heesakkers, J and van den Munckhof, E and Ghojazadeh, M and Rahnama'i, MS and Janssen, D}, title = {Differences in the Urinary Microbiome of Patients with Overactive Bladder Syndrome with and without Detrusor Overactivity on Urodynamic Measurements.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/life13051199}, pmid = {37240844}, issn = {2075-1729}, abstract = {INTRODUCTION: It has been hypothesized that the urinary microbiome might play an important role in OAB. Studies have been conducted on the association between OAB symptoms and the microbiome, although a possible causality still has to be determined.<br><br>MATERIAL AND METHODS: In this study, 12 female patients, &#x2265;18 years of age, with 'OAB DO+' and 9 female patients with 'OAB DO-' were included. Patients were excluded if they met one of the following exclusion criteria: bladder tumors and previous bladder operations; sacral neuromodulation; injection of Botox in the bladder; and TOT or TVT operations. Urine samples were collected and stored with patient informed consent and with the approval of the Hospital Ethical Review Board (Arnhem-Nijmegen). All OAB patients underwent urodynamics before collecting urine samples, and the diagnosis of detrusor overactivity was confirmed by two individual urologists. In addition, samples from 12 healthy controls who did not undergo urodynamic evaluation were analyzed. The 16S rRNA V1-V2 region amplification and gel electrophoresis were used to determine the microbiota.<br><br>RESULTS: 12 of the OAB patients had DO shown on their urodynamic studies; the remaining 9 patients had a normoactive detrusor on their urodynamic measurements. Overall, there were no substantial differences among the demographic characteristics of the subjects. The samples were classified as the following: 180 phyla, 180 classes, 179 orders, 178 families, 175 genera, and 138 species. The least commonly observed phyla were Proteobacteria, with an average presence of 10%, followed by Bacteroidetes with 15%, Actinobacteria with 16%, and Firmicutes with 41%. Most of the sequences could be classified according to the genus level for each sample.<br><br>DISCUSSION: Significant differences were observed in the urinary microbiome of patients with overactive bladder syndrome who have detrusor overactivity on urodynamics compared to OAB patients without detrusor overactivity and matched controls. OAB patients with detrusor overactivity have a significantly less diverse microbiome and show a higher proportion of Lactobacillus, particularly Lactobacillus iners. The results imply that the urinary microbiome could be involved in the pathogenesis of a specific phenotype of OAB. The urinary microbiome could be a new starting point to study the causes and treatments of OAB.}, }
@article {pmid37240769, year = {2023}, author = {Keathley, J and White, J and Reid, G}, title = {The Impact of Nutrition, Physical Activity, Beneficial Microbes, and Fecal Microbiota Transplant for Improving Health.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/life13051124}, pmid = {37240769}, issn = {2075-1729}, abstract = {The recognition that microbes are integral to human life has led to studies on how to manipulate them in favor of health outcomes. To date, there has been no conjoint recommendation for the intake of dietary compounds that can complement the ingested organisms in terms of promoting an improved health outcome. The aim of this review is to discuss how beneficial microbes in the form of probiotics, fermented foods, and donor feces are being used to manage health. In addition, we explore the rationale for selecting beneficial microbial strains and aligning diets to accommodate their propagation in the gut. A pilot clinical trial design is presented to examine the effects of probiotics and exercise in patients with phenylketonuria (PKU); it is the most common inborn error of amino acid metabolism, and it is a complication that requires lifelong dietary intervention. The example design is provided to illustrate the importance of using omics technology to see if the intervention elevates neuroactive biogenic amines in the plasma; increases the abundance of Eubacterium rectale, Coprococcus eutactus, Akkermansia muciniphila, or Butyricicoccus; and increases Escherichia/Shigella in the gut, all as markers of improved health. By emphasizing the combined importance of diet, microbial supplements, and the gut microbiome, we hope that future studies will better align these components, not only to improve outcomes, but also to enhance our understanding of the mechanisms.}, }
@article {pmid37240732, year = {2023}, author = {Belvedere, R and Novizio, N and Eletto, D and Porta, A and Di Maio, U and Petrella, A}, title = {The Protecting Activity of RIPACUT[®]: A New Therapeutic Approach Preserving Epithelial Health Based on the Combination of Iceland Lichen Extract, Silver Salt, and Sodium Hyaluronate.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/life13051088}, pmid = {37240732}, issn = {2075-1729}, abstract = {Epithelial integrity and function must be maintained in a dynamic healthy equilibrium, keeping unaltered the oxidative and inflammatory conditions and the microbiome of the cutaneous layers. Beside the skin, other mucous membranes can be injured, such as the nasal and anal ones, because of the contact with the external environment. Here, we detected the effects of RIPACUT[®], a combination of Iceland lichen extract, silver salt and sodium hyaluronate that individually act in diverse biological ways. The findings we obtained on keratinocytes, nasal and intestinal epithelial cells reveal that this combination showed a marked antioxidant activity, further assessed by the DPPH assay. Additionally, by analyzing the release of the IL-1β, TNF-α and IL-6 cytokines, we proved the anti-inflammatory effect of RIPACUT[®]. In both cases, the main preserving action was due to Iceland lichen. We also observed a notable antimicrobial activity mediated by the silver compound. These data suggest that RIPACUT[®] could signify the basis for an attractive pharmacological approach to maintaining healthy epithelial conditions. Interestingly, this may be extended to the nasal and anal areas where it protects against oxidative, inflammatory and infectious insults. Thus, these outcomes encourage the creation of sprays or creams for which sodium hyaluronate can guarantee a surface film-forming effect.}, }
@article {pmid37240731, year = {2023}, author = {Buey, B and Forcén, A and Grasa, L and Layunta, E and Mesonero, JE and Latorre, E}, title = {Gut Microbiota-Derived Short-Chain Fatty Acids: Novel Regulators of Intestinal Serotonin Transporter.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/life13051085}, pmid = {37240731}, issn = {2075-1729}, abstract = {Serotonin (5-HT) is a key neurotransmitter synthesized both in the gut and the central nervous system. It exerts its signaling through specific receptors (5-HTR), which regulate numerous behaviors and functions such as mood, cognitive function, platelet aggregation, gastrointestinal motility, and inflammation. Serotonin activity is determined mainly by the extracellular availability of 5-HT, which is controlled by the serotonin transporter (SERT). Recent studies indicate that, by activation of innate immunity receptors, gut microbiota can modulate serotonergic signaling by SERT modulation. As part of its function, gut microbiota metabolize nutrients from diet to produce different by-products, including short-chain fatty acids (SCFAs): propionate, acetate, and butyrate. However, it is not known whether these SCFAs regulate the serotonergic system. The objective of this study was to analyze the effect of SCFAs on the gastrointestinal serotonergic system using the Caco-2/TC7 cell line that expresses SERT and several receptors constitutively. Cells were treated with different SCFAs concentrations, and SERT function and expression were evaluated. In addition, the expression of 5-HT receptors 1A, 2A, 2B, 3A, 4, and 7 was also studied. Our results show that the microbiota-derived SCFAs regulate intestinal serotonergic system, both individually and in combination, modulating the function and expression of SERT and the 5-HT1A, 5-HT2B, and 5-HT7 receptors expression. Our data highlight the role of gut microbiota in the modulation of intestinal homeostasis and suggest microbiome modulation as a potential therapeutic treatment for intestinal pathologies and neuropsychiatric disorders involving serotonin.}, }
@article {pmid37240707, year = {2023}, author = {Witte, MB and Saupe, J and Reiner, J and Bannert, K and Schafmayer, C and Lamprecht, G and Berlin, P}, title = {Ileocolonic Healing after Small Ileocecal Resection in Mice: NOD2 Deficiency Impairs Anastomotic Healing by Local Mechanisms.}, journal = {Journal of clinical medicine}, volume = {12}, number = {10}, pages = {}, doi = {10.3390/jcm12103601}, pmid = {37240707}, issn = {2077-0383}, abstract = {Ileocecal resection (ICR) is frequently performed in Crohn's disease (CD). NOD2 mutations are risk factors for CD. Nod2 knockout (ko) mice show impaired anastomotic healing after extended ICR. We further investigated the role of NOD2 after limited ICR. C57B16/J (wt) and Nod2 ko littermates underwent limited ICR including 1-2 cm terminal ileum and were randomly assigned to vehicle or MDP treatment. Bursting pressure was measured on POD 5, and the anastomosis was analyzed for matrix turn-over and granulation tissue. Wound fibroblasts from subcutaneously implanted sponges were used for comparison. The M1/M2 macrophage plasma cytokines were analyzed. Mortality was not different between groups. Bursting pressure was significantly decreased in ko mice. This was associated with less granulation tissue but was not affected by MDP. However, anastomotic leak (AL) rate tended to be lower in MDP-treated ko mice (29% vs. 11%, p = 0.07). mRNA expression of collagen-1α (col1 α), collagen-3α (col3 α), matrix metalloproteinase (mmp)2 and mmp9 was increased in ko mice, indicating increased matrix turn-over, specifically in the anastomosis. Systemic TNF-α expression was significantly lower in ko mice. Ileocolonic healing is impaired in Nod2 ko mice after limited ICR by local mechanisms maybe including local dysbiosis.}, }
@article {pmid37240476, year = {2023}, author = {Tomita, T and Fukui, H and Okugawa, T and Nakanishi, T and Mieno, M and Nakai, K and Eda, H and Kitayama, Y and Oshima, T and Shinzaki, S and Miwa, H}, title = {Effect of Bifidobacterium bifidum G9-1 on the Intestinal Environment and Diarrhea-Predominant Irritable Bowel Syndrome (IBS-D)-like Symptoms in Patients with Quiescent Crohn's Disease: A Prospective Pilot Study.}, journal = {Journal of clinical medicine}, volume = {12}, number = {10}, pages = {}, doi = {10.3390/jcm12103368}, pmid = {37240476}, issn = {2077-0383}, abstract = {Diarrhea-predominant irritable bowel syndrome (IBS-D)-like symptoms are distressing for patients with quiescent Crohn's disease (qCD) and worsen their quality of life. In the present study, we assessed the effect of the probiotic Bifidobacterium bifidum G9-1 (BBG9-1) on the intestinal environment and clinical features in patients with qCD. Eleven patients with qCD, who met the Rome III diagnostic criteria for IBS-D, received BBG9-1 (24 mg) orally three times daily for 4 weeks. Indices of the intestinal environment (fecal calprotectin level and gut microbiome) and clinical features (CD/IBS-related symptoms, quality of life and stool irregularities) were evaluated before and after treatment. Treatment with BBG9-1 tended to reduce the IBS severity index in the studied patients (p = 0.07). Among gastrointestinal symptoms, abdominal pain and dyspepsia tended to be improved by the BBG9-1 treatment (p = 0.07 and p = 0.07, respectively), and IBD-related QOL showed a significant improvement (p = 0.007). With regard to mental status, the patient anxiety score was significantly lower at the endpoint of BBG9-1 treatment than at the baseline (p = 0.03). Although BBG9-1 treatment did not affect the fecal calprotectin level, it suppressed the serum MCP-1 level significantly and increased the abundance of intestinal Bacteroides in the study patients. The probiotic BBG9-1 is able to improve IBD-related QOL with a reduction of anxiety score in patients with quiescent CD and IBS-D-like symptoms.}, }
@article {pmid37240434, year = {2023}, author = {Nesci, A and Carnuccio, C and Ruggieri, V and D'Alessandro, A and Di Giorgio, A and Santoro, L and Gasbarrini, A and Santoliquido, A and Ponziani, FR}, title = {Gut Microbiota and Cardiovascular Disease: Evidence on the Metabolic and Inflammatory Background of a Complex Relationship.}, journal = {International journal of molecular sciences}, volume = {24}, number = {10}, pages = {}, doi = {10.3390/ijms24109087}, pmid = {37240434}, issn = {1422-0067}, abstract = {Several studies in recent years have demonstrated that gut microbiota-host interactions play an important role in human health and disease, including inflammatory and cardiovascular diseases. Dysbiosis has been linked to not only well-known inflammatory diseases, such as inflammatory bowel diseases, rheumatoid arthritis, and systemic lupus erythematous, but also to cardiovascular risk factors, such as atherosclerosis, hypertension, heart failure, chronic kidney disease, obesity, and type 2 diabetes mellitus. The ways the microbiota is involved in modulating cardiovascular risk are multiple and not only related to inflammatory mechanisms. Indeed, human and the gut microbiome cooperate as a metabolically active superorganism, and this affects host physiology through metabolic pathways. In turn, congestion of the splanchnic circulation associated with heart failure, edema of the intestinal wall, and altered function and permeability of the intestinal barrier result in the translocation of bacteria and their products into the systemic circulation, further enhancing the pro-inflammatory conditions underlying cardiovascular disorders. The aim of the present review is to describe the complex interplay between gut microbiota, its metabolites, and the development and evolution of cardiovascular diseases. We also discuss the possible interventions intended to modulate the gut microbiota to reduce cardiovascular risk.}, }
@article {pmid37240429, year = {2023}, author = {Baslam, A and Aitbaba, A and Lamrani Hanchi, A and Tazart, Z and Aboufatima, R and Soraa, N and Ait-El-Mokhtar, M and Boussaa, S and Baslam, M and Chait, A}, title = {Modulation of Gut Microbiome in Ecstasy/MDMA-Induced Behavioral and Biochemical Impairment in Rats and Potential of Post-Treatment with Anacyclus pyrethrum L. Aqueous Extract to Mitigate Adverse Effects.}, journal = {International journal of molecular sciences}, volume = {24}, number = {10}, pages = {}, doi = {10.3390/ijms24109086}, pmid = {37240429}, issn = {1422-0067}, abstract = {The use of illicit substances continues to pose a substantial threat to global health, affecting millions of individuals annually. Evidence suggests the existence of a 'brain-gut axis' as the involving connection between the central nervous system and gut microbiome (GM). Dysbiosis of the GM has been associated with the pathogenesis of various chronic diseases, including metabolic, malignant, and inflammatory conditions. However, little is currently known about the involvement of this axis in modulating the GM in response to psychoactive substances. In this study, we investigated the effect of MDMA (3,4-methylenedioxymethamphetamine, "Ecstasy")-dependence on the behavioral and biochemical responses, and the diversity and abundance of the gut microbiome in rats post-treated (or not) with aqueous extract of Anacyclus pyrethrum (AEAP), which has been reported to exhibit anticonvulsant activity. The dependency was validated using the conditioned place preference (CPP) paradigm, behavioral, and biochemical tests, while the gut microbiota was identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The CPP and behavioral tests confirmed the presence of MDMA withdrawal syndrome. Interestingly, treatment with AEAP led to a compositional shift in the GM compared to the MDMA-treated rats. Specifically, the AEAP group yielded a higher relative abundance of Lactobacillus and Bifidobacter, while animals receiving MDMA had higher levels of E. coli. These findings suggest that A. pyrethrum therapy may directly modulate the gut microbiome, highlighting a potential target for regulating and treating substance use disorders.}, }
@article {pmid37240357, year = {2023}, author = {Wu, H and Van Der Pol, WJ and Dubois, LG and Morrow, CD and Tollefsbol, TO}, title = {Dietary Supplementation of Inulin Contributes to the Prevention of Estrogen Receptor-Negative Mammary Cancer by Alteration of Gut Microbial Communities and Epigenetic Regulations.}, journal = {International journal of molecular sciences}, volume = {24}, number = {10}, pages = {}, doi = {10.3390/ijms24109015}, pmid = {37240357}, issn = {1422-0067}, support = {NCI R01 CA178441/NH/NIH HHS/United States ; NCI R01 CA204346/NH/NIH HHS/United States ; }, abstract = {Breast cancer (BC) is among the most frequently diagnosed malignant cancers in women in the United States. Diet and nutrition supplementation are closely related to BC onset and progression, and inulin is commercially available as a health supplement to improve gut health. However, little is known with respect to inulin intake for BC prevention. We investigated the effect of an inulin-supplemented diet on the prevention of estrogen receptor-negative mammary carcinoma in a transgenic mouse model. Plasma short-chain fatty acids were measured, the gut microbial composition was analyzed, and the expression of proteins related to cell cycle and epigenetics-related genes was measured. Inulin supplementation greatly inhibited tumor growth and significantly delayed tumor latency. The mice that consumed inulin had a distinct microbiome and higher diversity of gut microbial composition compared to the control. The concentration of propionic acid in plasma was significantly higher in the inulin-supplemented group. The protein expression of epigenetic-modulating histone deacetylase 2 (Hdac2), Hdac8, and DNA methyltransferase 3b decreased. The protein expression of factors related to tumor cell proliferation and survival, such as Akt, phospho-PI3K, and NF-kB, also decreased with inulin administration. Furthermore, sodium propionate showed BC prevention effect in vivo through epigenetic regulations. These studies suggest that modulating microbial composition through inulin consumption may be a promising strategy for BC prevention.}, }
@article {pmid37240180, year = {2023}, author = {Lafleur, S and Bodein, A and Mbuya Malaïka Mutombo, J and Mathieu, A and Joly Beauparlant, C and Minne, X and Chandad, F and Droit, A and Houde, VP}, title = {Multi-Omics Data Integration Reveals Key Variables Contributing to Subgingival Microbiome Dysbiosis-Induced Inflammatory Response in a Hyperglycemic Microenvironment.}, journal = {International journal of molecular sciences}, volume = {24}, number = {10}, pages = {}, doi = {10.3390/ijms24108832}, pmid = {37240180}, issn = {1422-0067}, abstract = {Subgingival microbiome dysbiosis promotes the development of periodontitis, an irreversible chronic inflammatory disease associated with metabolic diseases. However, studies regarding the effects of a hyperglycemic microenvironment on host-microbiome interactions and host inflammatory response during periodontitis are still scarce. Here, we investigated the impacts of a hyperglycemic microenvironment on the inflammatory response and transcriptome of a gingival coculture model stimulated with dysbiotic subgingival microbiomes. HGF-1 cells overlaid with U937 macrophage-like cells were stimulated with subgingival microbiomes collected from four healthy donors and four patients with periodontitis. Pro-inflammatory cytokines and matrix metalloproteinases were measured while the coculture RNA was submitted to a microarray analysis. Subgingival microbiomes were submitted to 16s rRNA gene sequencing. Data were analyzed using an advanced multi-omics bioinformatic data integration model. Our results show that the genes krt76, krt27, pnma5, mansc4, rab41, thoc6, tm6sf2, and znf506 as well as the pro-inflammatory cytokines IL-1β, GM-CSF, FGF2, IL-10, the metalloproteinases MMP3 and MMP8, and bacteria from the ASV 105, ASV 211, ASV 299, Prevotella, Campylobacter and Fretibacterium genera are key intercorrelated variables contributing to periodontitis-induced inflammatory response in a hyperglycemic microenvironment. In conclusion, our multi-omics integration analysis unveiled the complex interrelationships involved in the regulation of periodontal inflammation in response to a hyperglycemic microenvironment.}, }
@article {pmid37239914, year = {2023}, author = {Zhou, C and Gao, P and Wang, J}, title = {Comprehensive Analysis of Microbiome, Metabolome, and Transcriptome Revealed the Mechanisms of Intestinal Injury in Rainbow Trout under Heat Stress.}, journal = {International journal of molecular sciences}, volume = {24}, number = {10}, pages = {}, doi = {10.3390/ijms24108569}, pmid = {37239914}, issn = {1422-0067}, abstract = {Global warming is one of the most common environmental challenges faced by cold-water fish farming. Intestinal barrier function, gut microbiota, and gut microbial metabolites are significantly altered under heat stress, posing serious obstacles to the healthy artificial culture of rainbow trout. However, the molecular mechanisms underlying intestinal injury in rainbow trout under heat stress remain unclear. In the present study, the optimal growth temperature for rainbow trout (16 °C) was used for the control group, and the maximum temperature tolerated by rainbow trout (24 °C) was used for the heat stress group, which was subjected to heat stress for 21 days. The mechanism of intestinal injury in rainbow trout under heat stress was explored by combining animal histology, 16S rRNA gene amplicon sequencing, ultra-high performance liquid chromatography-mass spectrometry, and transcriptome sequencing. The results showed that the antioxidant capacity of rainbow trout was enhanced under heat stress, the levels of stress-related hormones were significantly increased, and the relative expression of genes related to heat stress proteins was significantly increased, indicating that the heat stress model of rainbow trout was successfully established. Secondly, the intestinal tract of rainbow trout showed inflammatory pathological characteristics under heat stress, with increased permeability, activation of the inflammatory factor signaling pathway, and increased relative expression of inflammatory factor genes, suggesting that the intestinal barrier function was impaired. Thirdly, heat stress caused an imbalance of intestinal commensal microbiota and changes in intestinal metabolites in rainbow trout, which participated in the stress response mainly by affecting lipid metabolism and amino acid metabolism. Finally, heat stress promoted intestinal injury in rainbow trout by activating the peroxisome proliferator-activated receptor-α signaling pathway. These results not only expand the understanding of fish stress physiology and regulation mechanisms, but also provide a scientific basis for healthy artificial culture and the reduction of rainbow trout production costs.}, }
@article {pmid37239571, year = {2023}, author = {Salazar, J and Durán, P and Díaz, MP and Chacín, M and Santeliz, R and Mengual, E and Gutiérrez, E and León, X and Díaz, A and Bernal, M and Escalona, D and Hernández, LAP and Bermúdez, V}, title = {Exploring the Relationship between the Gut Microbiota and Ageing: A Possible Age Modulator.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {10}, pages = {}, doi = {10.3390/ijerph20105845}, pmid = {37239571}, issn = {1660-4601}, abstract = {The gut microbiota (GM) has been the subject of intense research in recent years. Therefore, numerous factors affecting its composition have been thoroughly examined, and with them, their function and role in the individual's systems. The gut microbiota's taxonomical composition dramatically impacts older adults' health status. In this regard, it could either extend their life expectancy via the modulation of metabolic processes and the immune system or, in the case of dysbiosis, predispose them to age-related diseases, including bowel inflammatory and musculoskeletal diseases and metabolic and neurological disorders. In general, the microbiome of the elderly tends to present taxonomic and functional changes, which can function as a target to modulate the microbiota and improve the health of this population. The GM of centenarians is unique, with the faculty-promoting metabolic pathways capable of preventing and counteracting the different processes associated with age-related diseases. The molecular mechanisms by which the microbiota can exhibit anti-ageing properties are mainly based on anti-inflammatory and antioxidant actions. This review focuses on analysing the current knowledge of gut microbiota characteristics and modifiers, its relationship with ageing, and the GM-modulating approaches to increase life expectancy.}, }
@article {pmid37239169, year = {2023}, author = {Laakso, EL and Ewais, T}, title = {A Holistic Perspective on How Photobiomodulation May Influence Fatigue, Pain, and Depression in Inflammatory Bowel Disease: Beyond Molecular Mechanisms.}, journal = {Biomedicines}, volume = {11}, number = {5}, pages = {}, doi = {10.3390/biomedicines11051497}, pmid = {37239169}, issn = {2227-9059}, abstract = {BACKGROUND: Numerous mechanisms, mostly molecular, have been tested and proposed for photobiomodulation. Photobiomodulation is finding a niche in the treatment of conditions that have no gold-standard treatment or only partially effective pharmacological treatment. Many chronic conditions are characterised by symptoms for which there is no cure or control and for which pharmaceuticals may add to the disease burden through side effects. To add quality to life, alternate methods of symptom management need to be identified.<br><br>OBJECTIVE: To demonstrate how photobiomodulation, through its numerous mechanisms, may offer an adjunctive therapy in inflammatory bowel disease. Rather than considering only molecular mechanisms, we take an overarching biopsychosocial approach to propose how existing evidence gleaned from other studies may underpin a treatment strategy of potential benefit to people with Crohn's disease and ulcerative colitis.<br><br>MAIN FINDINGS: In this paper, the authors have proposed the perspective that photobiomodulation, through an integrated effect on the neuroimmune and microbiome-gut-brain axis, has the potential to be effective in managing the fatigue, pain, and depressive symptoms of people with inflammatory bowel disease.}, }
@article {pmid37239112, year = {2023}, author = {Tabassum, A and Ali, A and Zahedi, FD and Ismail, NAS}, title = {Immunomodulatory Role of Vitamin D on Gut Microbiome in Children.}, journal = {Biomedicines}, volume = {11}, number = {5}, pages = {}, doi = {10.3390/biomedicines11051441}, pmid = {37239112}, issn = {2227-9059}, abstract = {Vitamin D plays a role in regulating the immune system and can be linked to the alteration of the gut microbiome, which leads to several immunological diseases. This systematic review aims to explore the relationship between Vitamin D and children's gut microbiome, as well as its impact towards the immune system. We have systematically collated relevant studies from different databases concerning changes in the gut microbiome of children from infants to 18 years old associated with Vitamin D and the immunological pathways. The studies utilized 16S rRNA sequencing analysis of fecal matter with or without Vitamin D supplementation and Vitamin D levels. Ten studies were selected for the review, among which eight studies showed significant alterations in the gut microbiome related to Vitamin D supplementation or Vitamin D levels. The taxa of the phylum Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria are the most altered in these studies. The alteration of the taxa alters the Th1 and Th2 pathways and changes the immune response. We will discuss how Vitamin D may contribute to the activation of immune pathways via its effects on intestinal barrier function, microbiome composition, and/or direct effects on immune responses. In conclusion, the studies examined in this review have provided evidence that Vitamin D levels may have an impact on the composition of children's gut microbiomes.}, }
@article {pmid37239063, year = {2023}, author = {Gong, J and Osipov, A and Lorber, J and Tighiouart, M and Kwan, AK and Muranaka, H and Akinsola, R and Billet, S and Levi, A and Abbas, A and Davelaar, J and Bhowmick, N and Hendifar, AE}, title = {Combination L-Glutamine with Gemcitabine and Nab-Paclitaxel in Treatment-Naïve Advanced Pancreatic Cancer: The Phase I GlutaPanc Study Protocol.}, journal = {Biomedicines}, volume = {11}, number = {5}, pages = {}, doi = {10.3390/biomedicines11051392}, pmid = {37239063}, issn = {2227-9059}, abstract = {Advanced pancreatic cancer is underscored by progressive therapeutic resistance and a dismal 5-year survival rate of 3%. Preclinical data demonstrated glutamine supplementation, not deprivation, elicited antitumor effects against pancreatic ductal adenocarcinoma (PDAC) alone and in combination with gemcitabine in a dose-dependent manner. The GlutaPanc phase I trial is a single-arm, open-label clinical trial investigating the safety of combination L-glutamine, gemcitabine, and nab-paclitaxel in subjects (n = 16) with untreated, locally advanced unresectable or metastatic pancreatic cancer. Following a 7-day lead-in phase with L-glutamine, the dose-finding phase via Bayesian design begins with treatment cycles lasting 28 days until disease progression, intolerance, or withdrawal. The primary objective is to establish the recommended phase II dose (RP2D) of combination L-glutamine, gemcitabine, and nab-paclitaxel. Secondary objectives include safety of the combination across all dose levels and preliminary evidence of antitumor activity. Exploratory objectives include evaluating changes in plasma metabolites across multiple time points and changes in the stool microbiome pre and post L-glutamine supplementation. If this phase I clinical trial demonstrates the feasibility of L-glutamine in combination with nab-paclitaxel and gemcitabine, we would advance the development of this combination as a first-line systemic option in subjects with metastatic pancreatic cancer, a high-risk subgroup desperately in need of additional therapies.}, }
@article {pmid37239059, year = {2023}, author = {Kunst, C and Schmid, S and Michalski, M and Tümen, D and Buttenschön, J and Müller, M and Gülow, K}, title = {The Influence of Gut Microbiota on Oxidative Stress and the Immune System.}, journal = {Biomedicines}, volume = {11}, number = {5}, pages = {}, doi = {10.3390/biomedicines11051388}, pmid = {37239059}, issn = {2227-9059}, abstract = {The human gastrointestinal tract is home to a complex microbial community that plays an important role in the general well-being of the entire organism. The gut microbiota generates a variety of metabolites and thereby regulates many biological processes, such as the regulation of the immune system. In the gut, bacteria are in direct contact with the host. The major challenge here is to prevent unwanted inflammatory reactions on one hand and on the other hand to ensure that the immune system can be activated when pathogens invade. Here the REDOX equilibrium is of utmost importance. This REDOX equilibrium is controlled by the microbiota either directly or indirectly via bacterial-derived metabolites. A balanced microbiome sorts for a stable REDOX balance, whereas dysbiosis destabilizes this equilibrium. An imbalanced REDOX status directly affects the immune system by disrupting intracellular signaling and promoting inflammatory responses. Here we (i) focus on the most common reactive oxygen species (ROS) and (ii) define the transition from a balanced REDOX state to oxidative stress. Further, we (iii) describe the role of ROS in regulating the immune system and inflammatory responses. Thereafter, we (iv) examine the influence of microbiota on REDOX homeostasis and how shifts in pro- and anti-oxidative cellular conditions can suppress or promote immune responses or inflammation.}, }
@article {pmid37239020, year = {2023}, author = {Guedes, BFS and Cardoso, SM and Esteves, AR}, title = {The Impact of microRNAs on Mitochondrial Function and Immunity: Relevance to Parkinson's Disease.}, journal = {Biomedicines}, volume = {11}, number = {5}, pages = {}, doi = {10.3390/biomedicines11051349}, pmid = {37239020}, issn = {2227-9059}, abstract = {Parkinson's Disease (PD), the second most common neurodegenerative disorder, is characterised by the severe loss of dopaminergic neurons in the Substantia Nigra pars compacta (SNpc) and by the presence of Lewy bodies. PD is diagnosed upon the onset of motor symptoms, such as bradykinesia, resting tremor, rigidity, and postural instability. It is currently accepted that motor symptoms are preceded by non-motor features, such as gastrointestinal dysfunction. In fact, it has been proposed that PD might start in the gut and spread to the central nervous system. Growing evidence reports that the gut microbiota, which has been found to be altered in PD patients, influences the function of the central and enteric nervous systems. Altered expression of microRNAs (miRNAs) in PD patients has also been reported, many of which regulate key pathological mechanisms involved in PD pathogenesis, such as mitochondrial dysfunction and immunity. It remains unknown how gut microbiota regulates brain function; however, miRNAs have been highlighted as important players. Remarkably, numerous studies have depicted the ability of miRNAs to modulate and be regulated by the host's gut microbiota. In this review, we summarize the experimental and clinical studies implicating mitochondrial dysfunction and immunity in PD. Moreover, we gather recent data on miRNA involvement in these two processes. Ultimately, we discuss the reciprocal crosstalk between gut microbiota and miRNAs. Studying the bidirectional interaction of gut microbiome-miRNA might elucidate the aetiology and pathogenesis of gut-first PD, which could lead to the application of miRNAs as potential biomarkers or therapeutical targets for PD.}, }
@article {pmid37238992, year = {2023}, author = {Trevellin, E and Bettini, S and Pilatone, A and Vettor, R and Milan, G}, title = {Obesity, the Adipose Organ and Cancer in Humans: Association or Causation?.}, journal = {Biomedicines}, volume = {11}, number = {5}, pages = {}, doi = {10.3390/biomedicines11051319}, pmid = {37238992}, issn = {2227-9059}, abstract = {Epidemiological observations, experimental studies and clinical data show that obesity is associated with a higher risk of developing different types of cancer; however, proof of a cause-effect relationship that meets the causality criteria is still lacking. Several data suggest that the adipose organ could be the protagonist in this crosstalk. In particular, the adipose tissue (AT) alterations occurring in obesity parallel some tumour behaviours, such as their theoretically unlimited expandability, infiltration capacity, angiogenesis regulation, local and systemic inflammation and changes to the immunometabolism and secretome. Moreover, AT and cancer share similar morpho-functional units which regulate tissue expansion: the adiponiche and tumour-niche, respectively. Through direct and indirect interactions involving different cellular types and molecular mechanisms, the obesity-altered adiponiche contributes to cancer development, progression, metastasis and chemoresistance. Moreover, modifications to the gut microbiome and circadian rhythm disruption also play important roles. Clinical studies clearly demonstrate that weight loss is associated with a decreased risk of developing obesity-related cancers, matching the reverse-causality criteria and providing a causality correlation between the two variables. Here, we provide an overview of the methodological, epidemiological and pathophysiological aspects, with a special focus on clinical implications for cancer risk and prognosis and potential therapeutic interventions.}, }
@article {pmid37238974, year = {2023}, author = {Tsuji, G and Yamamura, K and Kawamura, K and Kido-Nakahara, M and Ito, T and Nakahara, T}, title = {Novel Therapeutic Targets for the Treatment of Atopic Dermatitis.}, journal = {Biomedicines}, volume = {11}, number = {5}, pages = {}, doi = {10.3390/biomedicines11051303}, pmid = {37238974}, issn = {2227-9059}, abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin disease that significantly impacts quality of life. The pathogenesis of AD is a complex combination of skin barrier dysfunction, type II immune response, and pruritus. Progress in the understanding of the immunological mechanisms of AD has led to the recognition of multiple novel therapeutic targets. For systemic therapy, new biologic agents that target IL-13, IL-22, IL-33, the IL-23/IL-17 axis, and OX40-OX40L are being developed. Binding of type II cytokines to their receptors activates Janus kinase (JAK) and its downstream signal, namely signal transduction and activator of transcription (STAT). JAK inhibitors block the activation of the JAK-STAT pathway, thereby blocking the signaling pathways mediated by type II cytokines. In addition to oral JAK inhibitors, histamine H4 receptor antagonists are under investigation as small-molecule compounds. For topical therapy, JAK inhibitors, aryl hydrocarbon receptor modulators, and phosphodiesterase-4 inhibitors are being approved. Microbiome modulation is also being examined for the treatment of AD. This review outlines current and future directions for novel therapies of AD that are currently being investigated in clinical trials, focusing on their mechanisms of action and efficacy. This supports the accumulation of data on advanced treatments for AD in the new era of precision medicine.}, }
@article {pmid37238943, year = {2023}, author = {Shahbazi, A and Sepehrinezhad, A and Vahdani, E and Jamali, R and Ghasempour, M and Massoudian, S and Sahab Negah, S and Larsen, FS}, title = {Gut Dysbiosis and Blood-Brain Barrier Alteration in Hepatic Encephalopathy: From Gut to Brain.}, journal = {Biomedicines}, volume = {11}, number = {5}, pages = {}, doi = {10.3390/biomedicines11051272}, pmid = {37238943}, issn = {2227-9059}, abstract = {A common neuropsychiatric complication of advanced liver disease, hepatic encephalopathy (HE), impacts the quality of life and length of hospital stays. There is new evidence that gut microbiota plays a significant role in brain development and cerebral homeostasis. Microbiota metabolites are providing a new avenue of therapeutic options for several neurological-related disorders. For instance, the gut microbiota composition and blood-brain barrier (BBB) integrity are altered in HE in a variety of clinical and experimental studies. Furthermore, probiotics, prebiotics, antibiotics, and fecal microbiota transplantation have been shown to positively affect BBB integrity in disease models that are potentially extendable to HE by targeting gut microbiota. However, the mechanisms that underlie microbiota dysbiosis and its effects on the BBB are still unclear in HE. To this end, the aim of this review was to summarize the clinical and experimental evidence of gut dysbiosis and BBB disruption in HE and a possible mechanism.}, }
@article {pmid37238827, year = {2023}, author = {Törős, G and El-Ramady, H and Prokisch, J and Velasco, F and Llanaj, X and Nguyen, DHH and Peles, F}, title = {Modulation of the Gut Microbiota with Prebiotics and Antimicrobial Agents from Pleurotus ostreatus Mushroom.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {10}, pages = {}, doi = {10.3390/foods12102010}, pmid = {37238827}, issn = {2304-8158}, abstract = {Pleurotus ostreatus (Jacq. ex Fr.) P. Kumm mushroom contains bioactive compounds with both antimicrobial and prebiotic properties, which are distributed in the mushroom mycelium, fruiting body, and spent substrate. The mushroom is rich in nondigestible carbohydrates like chitin and glucan, which act as prebiotics and support the growth and activity of beneficial gut bacteria, thereby maintaining a healthy balance of gut microbiota and reducing the risk of antibiotic resistance. The bioactive compounds in P. ostreatus mushrooms, including polysaccharides (glucans, chitin) and secondary metabolites (phenolic compounds, terpenoids, and lectins), exhibit antibacterial, antiviral, and antifungal activities. When mushrooms are consumed, these compounds can help preventing the growth and spread of harmful bacteria in the gut, reducing the risk of infections and the development of antibiotic resistance. Nonetheless, further research is necessary to determine the efficacy of P. ostreatus against different pathogens and to fully comprehend its prebiotic and antimicrobial properties. Overall, consuming a diet rich in mushroom-based foods can have a positive impact on human digestion health. A mushroom-based diet can support a healthy gut microbiome and reduce the need for antibiotics.}, }
@article {pmid37238799, year = {2023}, author = {Dimitriou, TG and Asoutis Didaras, N and Barda, C and Skopeliti, D and Kontogianni, K and Karatasou, K and Skaltsa, H and Mossialos, D}, title = {Antiviral Activity of Beebread, Bee-Collected Pollen and Artificially Fermented Follen against Influenza A Virus.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {10}, pages = {}, doi = {10.3390/foods12101978}, pmid = {37238799}, issn = {2304-8158}, abstract = {Bee-collected pollen (BCP) and the naturally fermented BCP product known as bee bread (BB) are functional foods renowned for their nutritious, antioxidant, antibacterial and other therapeutic properties. This is the first study employed to assess the antiviral activity of BCP and BB against influenza A virus (IAV) H1N1 along with their proteinaceous, aqueous and n-butanol fractions. Additionally, artificially fermented BCP has been evaluated against IAV (H1N1). Antiviral activity was assessed in vitro by comparative real-time PCR assay. IC50 values ranged from 0.022 to 10.04 mg/mL, and Selectivity Index (SI) values ranged from 1.06 to 338.64. Artificially fermented BCP samples AF5 and AF17 demonstrated higher SI values than unfermented BCP, and proteinaceous fractions demonstrated the highest SI values. The chemical profile of BCP and BB samples, analyzed using NMR and LC-MS, revealed the presence of specialized metabolites that may contribute toward the antiviral activity. Overall, the significant anti-IAV activity of BB and BCP harvested in Thessaly (Greece) could be attributed to chemical composition (especially undiscovered yet proteinaceous compounds) and possibly to microbiome metabolism. Further research regarding the antiviral properties of BCP and BB will elucidate the mode of action and could lead to new treatments against IAV or other viral diseases.}, }
@article {pmid37238769, year = {2023}, author = {Stanzer, D and Hanousek Čiča, K and Blesić, M and Smajić Murtić, M and Mrvčić, J and Spaho, N}, title = {Alcoholic Fermentation as a Source of Congeners in Fruit Spirits.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {10}, pages = {}, doi = {10.3390/foods12101951}, pmid = {37238769}, issn = {2304-8158}, abstract = {Fermentation is a crucial process in the production of alcoholic beverages such as spirits, which produces a number of volatile compounds due to the metabolic activities of yeast. These volatile compounds, together with the volatile components of the raw materials and the volatile compounds produced during the distillation and aging process, play a crucial role in determining the final flavor and aroma of spirits. In this manuscript, we provide a comprehensive overview of yeast fermentation and the volatile compounds produced during alcoholic fermentation. We will establish a link between the microbiome and volatile compounds during alcoholic fermentation and describe the various factors that influence volatile compound production, including yeast strain, temperature, pH, and nutrient availability. We will also discuss the effects of these volatile compounds on the sensory properties of spirits and describe the major aroma compounds in these alcoholic beverages.}, }
@article {pmid37238716, year = {2023}, author = {Sharma, A and Yu, Y and Lu, J and Lu, L and Zhang, YG and Xia, Y and Sun, J and Claud, EC}, title = {The Impact of Maternal Probiotics on Intestinal Vitamin D Receptor Expression in Early Life.}, journal = {Biomolecules}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/biom13050847}, pmid = {37238716}, issn = {2218-273X}, support = {DK105118/DK/NIDDK NIH HHS/United States ; DK114126/DK/NIDDK NIH HHS/United States ; }, abstract = {Vitamin D signaling via the Vitamin D Receptor (VDR) has been shown to protect against intestinal inflammation. Previous studies have also reported the mutual interactions of intestinal VDR and the microbiome, indicating a potential role of probiotics in modulating VDR expression. In preterm infants, although probiotics have been shown to reduce the incidence of necrotizing enterocolitis (NEC), they are not currently recommended by the FDA due to potential risks in this population. No previous studies have delved into the effect of maternally administered probiotics on intestinal VDR expression in early life. Using an infancy mouse model, we found that young mice exposed to maternally administered probiotics (SPF/LB) maintained higher colonic VDR expression than our unexposed mice (SPF) in the face of a systemic inflammatory stimulus. These findings indicate a potential role for microbiome-modulating therapies in preventing diseases such as NEC through the enhancement of VDR signaling.}, }
@article {pmid37238685, year = {2023}, author = {Smędra, A and Berent, J}, title = {The Influence of the Oral Microbiome on Oral Cancer: A Literature Review and a New Approach.}, journal = {Biomolecules}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/biom13050815}, pmid = {37238685}, issn = {2218-273X}, abstract = {In our recent article (Smędra et al.: Oral form of auto-brewery syndrome. J Forensic Leg Med. 2022; 87: 102333), we showed that alcohol production can occur in the oral cavity (oral auto-brewery syndrome) due to a disruption in the microbiota (dysbiosis). An intermediate step on the path leading to the formation of alcohol is acetaldehyde. Typically, acetic aldehyde is transformed into acetate particles inside the human body via acetaldehyde dehydrogenase. Unfortunately, acetaldehyde dehydrogenase activity is low in the oral cavity, and acetaldehyde remains there for a long time. Since acetaldehyde is a recognised risk factor for squamous cell carcinoma arising from the oral cavity, we decided to analyse the relationship linking the oral microbiome, alcohol, and oral cancer using the narrative review method, based on browsing articles in the PubMed database. In conclusion, enough evidence supports the speculation that oral alcohol metabolism must be assessed as an independent carcinogenic risk. We also hypothesise that dysbiosis and the production of acetaldehyde from non-alcoholic food and drinks should be treated as a new factor for the development of cancer.}, }
@article {pmid37238268, year = {2023}, author = {Song, Y and Kim, MS and Chung, J and Na, HS}, title = {Simultaneous Analysis of Bacterial and Fungal Communities in Oral Samples from Intubated Patients in Intensive Care Unit.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {13}, number = {10}, pages = {}, doi = {10.3390/diagnostics13101784}, pmid = {37238268}, issn = {2075-4418}, abstract = {Intubated patients in intensive care units (ICUs) too frequently contract ventilator-associated pneumonia or Candida infections. Oropharyngeal microbes are believed to play an important etiologic role. This study was undertaken to determine whether next-generation sequencing (NGS) can be used to simultaneously analyze bacterial and fungal communities. Buccal samples were collected from intubated ICU patients. Primers targeting the V1-V2 region of bacterial 16S rRNA and the internal transcribed spacer 2 (ITS2) region of fungal 18S rRNA were used. V1-V2, ITS2, or mixed V1-V2/ITS2 primers were used to prepare an NGS library. Bacterial and fungal relative abundances were comparable for V1-V2, ITS2, or mixed V1-V2/ITS2 primers, respectively. A standard microbial community was used to adjust the relative abundances to theoretical abundance, and NGS and RT-PCR-adjusted relative abundances showed a high correlation. Using mixed V1-V2/ITS2 primers, bacterial and fungal abundances were simultaneously determined. The constructed microbiome network revealed novel interkingdom and intrakingdom interactions, and the simultaneous detection of bacterial and fungal communities using mixed V1-V2/ITS2 primers enabled analysis across two kingdoms. This study provides a novel approach to simultaneously determining bacterial and fungal communities using mixed V1-V2/ITS2 primers.}, }
@article {pmid37238082, year = {2023}, author = {Matthews, C and Walsh, AM and Gordon, SV and Markey, B and Cotter, PD and O' Mahony, J}, title = {Differences in Faecal Microbiome Taxonomy, Diversity and Functional Potential in a Bovine Cohort Experimentally Challenged with Mycobacterium avium subsp. paratuberculosis (MAP).}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {10}, pages = {}, doi = {10.3390/ani13101652}, pmid = {37238082}, issn = {2076-2615}, abstract = {Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of Johne's disease in ruminants, a chronic enteritis which results in emaciation and eventual loss of the animal. Recent advances in metagenomics have allowed a more in-depth study of complex microbiomes, including that of gastrointestinal tracts, and have the potential to provide insights into consequences of the exposure of an animal to MAP or other pathogens. This study aimed to investigate taxonomic diversity and compositional changes of the faecal microbiome of cattle experimentally challenged with MAP compared to an unexposed control group. Faecal swab samples were collected from a total of 55 animals [exposed group (n = 35) and a control group (n = 20)], across three time points (months 3, 6 and 9 post-inoculation). The composition and functional potential of the faecal microbiota differed across time and between the groups (p < 0.05), with the primary differences, from both a taxonomic and functional perspective, occurring at 3 months post inoculation. These included significant differences in the relative abundance of the genera Methanobrevibacter and Bifidobacterium and also of 11 other species (4 at a higher relative abundance in the exposed group and 7 at a higher relative abundance in the control group). Correlations were made between microbiome data and immunopathology measurements and it was noted that changes in the microbial composition correlated with miRNA-155, miR-146b and IFN-ɣ. In summary, this study illustrates the impact of exposure to MAP on the ruminant faecal microbiome with a number of species that may have relevance in veterinary medicine for tracking exposure to MAP.}, }
@article {pmid37238057, year = {2023}, author = {Dittoe, DK and Johnson, CN and Byrd, JA and Ricke, SC and Piva, A and Grilli, E and Swaggerty, CL}, title = {Impact of a Blend of Microencapsulated Organic Acids and Botanicals on the Microbiome of Commercial Broiler Breeders under Clinical Necrotic Enteritis.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {10}, pages = {}, doi = {10.3390/ani13101627}, pmid = {37238057}, issn = {2076-2615}, abstract = {Previously, the supplementation of a microencapsulated blend of organic acids and botanicals improved the health and performance of broiler breeders under non-challenged conditions. This study aimed to determine if the microencapsulated blend impacted dysbiosis and necrotic enteritis (NE) in broiler breeders. Day-of-hatch chicks were assigned to non-challenge and challenge groups, provided a basal diet supplemented with 0 or 500 g/MT of the blend, and subjected to a laboratory model for NE. On d 20-21, jejunum/ileum content were collected for microbiome sequencing (n = 10; V4 region of 16S rRNA gene). The experiment was repeated (n = 3), and data were analyzed in QIIME2 and R. Alpha and beta diversity, core microbiome, and compositional differences were determined (significance at p ≤ 0.05; Q ≤ 0.05). There was no difference between richness and evenness of those fed diets containing 0 and 500 g/MT microencapsulated blend, but differences were seen between the non-challenged and challenged groups. Beta diversity of the 0 and 500 g/MT non-challenged groups differed, but no differences existed between the NE-challenged groups. The core microbiome of those fed 500 g/MT similarly consisted of Lactobacillus and Clostridiaceae. Furthermore, challenged birds fed diets containing 500 g/MT had a higher abundance of significantly different phyla, namely, Actinobacteriota, Bacteroidota, and Verrucomicrobiota, than the 0 g/MT challenged group. Dietary supplementation of a microencapsulated blend shifted the microbiome by supporting beneficial and core taxa.}, }
@article {pmid37238002, year = {2023}, author = {Weaver, CM and Ferruzzi, MG and Maiz, M and Cladis, DP and Nakatsu, CH and McCabe, GP and Lila, MA}, title = {Crop, Host, and Gut Microbiome Variation Influence Precision Nutrition: An Example of Blueberries.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, doi = {10.3390/antiox12051136}, pmid = {37238002}, issn = {2076-3921}, support = {R01AT008754/NH/NIH HHS/United States ; }, abstract = {Epidemiological studies have shown associations between polyphenol-rich fruit intake and bone health, and preclinical studies have shown that blueberries improve bone health. To determine the genotype and dose of blueberries that are effective in ameliorating age-related bone loss, a multi-institutional team of investigators performed in vitro, preclinical, and clinical studies on blueberry varieties that differed in flavonoid profiles. Principal component analysis was used to select blueberry genotypes that varied in anthocyanin profiles. Total phenolic content did not predict the bioavailability of polyphenolic compounds in rats. A range in bioavailability was observed in individual polyphenolic compounds across genotypes. Both alpha and beta diversity analyses indicated that gut microbiome profiles varied with blueberry dose in rats. Additionally, the identification of specific taxa, such as Prevotellaceae_UCG-001 and Coriobacteriales, increasing after blueberry consumption adds to the mounting evidence of their role in polyphenol metabolism. All of the sources of variation can inform blueberry breeding practices to influence precision nutrition.}, }
@article {pmid37237983, year = {2023}, author = {Ravenhill, SM and Evans, AH and Crewther, SG}, title = {Escalating Bi-Directional Feedback Loops between Proinflammatory Microglia and Mitochondria in Ageing and Post-Diagnosis of Parkinson's Disease.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, doi = {10.3390/antiox12051117}, pmid = {37237983}, issn = {2076-3921}, abstract = {Parkinson's disease (PD) is a chronic and progressive age-related neurodegenerative disease affecting up to 3% of the global population over 65 years of age. Currently, the underlying physiological aetiology of PD is unknown. However, the diagnosed disorder shares many common non-motor symptoms associated with ageing-related neurodegenerative disease progression, such as neuroinflammation, microglial activation, neuronal mitochondrial impairment, and chronic autonomic nervous system dysfunction. Clinical PD has been linked to many interrelated biological and molecular processes, such as escalating proinflammatory immune responses, mitochondrial impairment, lower adenosine triphosphate (ATP) availability, increasing release of neurotoxic reactive oxygen species (ROS), impaired blood brain barrier integrity, chronic activation of microglia, and damage to dopaminergic neurons consistently associated with motor and cognitive decline. Prodromal PD has also been associated with orthostatic hypotension and many other age-related impairments, such as sleep disruption, impaired gut microbiome, and constipation. Thus, this review aimed to present evidence linking mitochondrial dysfunction, including elevated oxidative stress, ROS, and impaired cellular energy production, with the overactivation and escalation of a microglial-mediated proinflammatory immune response as naturally occurring and damaging interlinked bidirectional and self-perpetuating cycles that share common pathological processes in ageing and PD. We propose that both chronic inflammation, microglial activation, and neuronal mitochondrial impairment should be considered as concurrently influencing each other along a continuum rather than as separate and isolated linear metabolic events that affect specific aspects of neural processing and brain function.}, }
@article {pmid37237848, year = {2023}, author = {Fan, N and Fusco, JL and Rosenberg, DW}, title = {Antioxidant and Anti-Inflammatory Properties of Walnut Constituents: Focus on Personalized Cancer Prevention and the Microbiome.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, doi = {10.3390/antiox12050982}, pmid = {37237848}, issn = {2076-3921}, support = {1 R01 CA252045-01A1/NH/NIH HHS/United States ; }, abstract = {Walnuts have been lauded as a 'superfood', containing a remarkable array of natural constituents that may have additive and/or synergistic properties that contribute to reduced cancer risk. Walnuts are a rich source of polyunsaturated fatty acids (PUFAs: alpha-linolenic acid, ALA), tocopherols, antioxidant polyphenols (including ellagitannins), and prebiotics, including fiber (2 g/oz). There is a growing body of evidence that walnuts may contribute in a positive way to the gut microbiome, having a prebiotic potential that promotes the growth of beneficial bacteria. Studies supporting this microbiome-modifying potential include both preclinical cancer models as well as several promising human clinical trials. Mediated both directly and indirectly via its actions on the microbiome, many of the beneficial properties of walnuts are related to a range of anti-inflammatory properties, including powerful effects on the immune system. Among the most potent constituents of walnuts are the ellagitannins, primarily pedunculagin. After ingestion, the ellagitannins are hydrolyzed at low pH to release ellagic acid (EA), a non-flavonoid polyphenolic that is subsequently metabolized by the microbiota to the bioactive urolithins (hydroxydibenzo[b,d]pyran-6-ones). Several urolithins, including urolithin A, reportedly have potent anti-inflammatory properties. These properties of walnuts provide the rationale for including this tree nut as part of a healthy diet for reducing overall disease risk, including colorectal cancer. This review considers the latest information regarding the potential anti-cancer and antioxidant properties of walnuts and how they may be incorporated into the diet to provide additional health benefits.}, }
@article {pmid37237771, year = {2023}, author = {Airola, C and Severino, A and Porcari, S and Fusco, W and Mullish, BH and Gasbarrini, A and Cammarota, G and Ponziani, FR and Ianiro, G}, title = {Future Modulation of Gut Microbiota: From Eubiotics to FMT, Engineered Bacteria, and Phage Therapy.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, doi = {10.3390/antibiotics12050868}, pmid = {37237771}, issn = {2079-6382}, abstract = {The human gut is inhabited by a multitude of bacteria, yeasts, and viruses. A dynamic balance among these microorganisms is associated with the well-being of the human being, and a large body of evidence supports a role of dysbiosis in the pathogenesis of several diseases. Given the importance of the gut microbiota in the preservation of human health, probiotics, prebiotics, synbiotics, and postbiotics have been classically used as strategies to modulate the gut microbiota and achieve beneficial effects for the host. Nonetheless, several molecules not typically included in these categories have demonstrated a role in restoring the equilibrium among the components of the gut microbiota. Among these, rifaximin, as well as other antimicrobial drugs, such as triclosan, or natural compounds (including evodiamine and polyphenols) have common pleiotropic characteristics. On one hand, they suppress the growth of dangerous bacteria while promoting beneficial bacteria in the gut microbiota. On the other hand, they contribute to the regulation of the immune response in the case of dysbiosis by directly influencing the immune system and epithelial cells or by inducing the gut bacteria to produce immune-modulatory compounds, such as short-chain fatty acids. Fecal microbiota transplantation (FMT) has also been investigated as a procedure to restore the equilibrium of the gut microbiota and has shown benefits in many diseases, including inflammatory bowel disease, chronic liver disorders, and extraintestinal autoimmune conditions. One of the most significant limits of the current techniques used to modulate the gut microbiota is the lack of tools that can precisely modulate specific members of complex microbial communities. Novel approaches, including the use of engineered probiotic bacteria or bacteriophage-based therapy, have recently appeared as promising strategies to provide targeted and tailored therapeutic modulation of the gut microbiota, but their role in clinical practice has yet to be clarified. The aim of this review is to discuss the most recently introduced innovations in the field of therapeutic microbiome modulation.}, }
@article {pmid37237698, year = {2023}, author = {Graspeuntner, S and Koethke, K and Scholz, C and Semmler, L and Lupatsii, M and Kirchhoff, L and Herrmann, J and Rox, K and Wittstein, K and Käding, N and Hanker, LC and Stadler, M and Brönstrup, M and Müller, R and Shima, K and Rupp, J}, title = {Sorangicin A Is Active against Chlamydia in Cell Culture, Explanted Fallopian Tubes, and Topical In Vivo Treatment.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, doi = {10.3390/antibiotics12050795}, pmid = {37237698}, issn = {2079-6382}, abstract = {Current treatment of Chlamydia trachomatis using doxycycline and azithromycin introduces detrimental side effects on the host's microbiota. As a potential alternative treatment, the myxobacterial natural product sorangicin A (SorA) blocks the bacterial RNA polymerase. In this study we analyzed the effectiveness of SorA against C. trachomatis in cell culture, and explanted fallopian tubes and systemic and local treatment in mice, providing also pharmacokinetic data on SorA. Potential side effects of SorA on the vaginal and gut microbiome were assessed in mice and against human-derived Lactobacillus species. SorA showed minimal inhibitory concentrations of 80 ng/mL (normoxia) to 120 ng/mL (hypoxia) against C. trachomatis in vitro and was eradicating C. trachomatis at a concentration of 1 µg/mL from fallopian tubes. In vivo, SorA reduced chlamydial shedding by more than 100-fold within the first days of infection by topical application corresponding with vaginal detection of SorA only upon topical treatment, but not after systemic application. SorA changed gut microbial composition during intraperitoneal application only and did neither alter the vaginal microbiota in mice nor affect growth of human-derived lactobacilli. Additional dose escalations and/or pharmaceutical modifications will be needed to optimize application of SorA and to reach sufficient anti-chlamydial activity in vivo.}, }
@article {pmid37237477, year = {2023}, author = {Ramirez-Villacis, DX and Erazo-Garcia, P and Quijia-Pillajo, J and Llerena-Llerena, S and Barriga-Medina, N and Jones, CD and Leon-Reyes, A}, title = {Influence of Grafting on Rootstock Rhizosphere Microbiome Assembly in Rosa sp. 'Natal Brier'.}, journal = {Biology}, volume = {12}, number = {5}, pages = {}, doi = {10.3390/biology12050663}, pmid = {37237477}, issn = {2079-7737}, abstract = {The root microbiome is vital in plant development and health and is highly influenced by crop cultural practices. Rose (Rosa sp.) is the most popular cut flower worldwide. Grafting in rose production is a standard practice to increase yield, improve flower quality, or reduce root-associated pests and diseases. 'Natal Brier' is a standard rootstock used in most commercial operations in Ecuador and Colombia, leading countries in producing and exporting ornamentals. It is known that the rose scion genotype affects root biomass and the root exudate profile of grafted plants. However, little is known about the influence of the rose scion genotype on the rhizosphere microbiome. We examined the influence of grafting and scion genotype on the rhizosphere microbiome of the rootstock 'Natal Brier'. The microbiomes of the non-grafted rootstock and the rootstock grafted with two red rose cultivars were assessed using 16S rRNA and ITS sequencing. Grafting changed microbial community structure and function. Further, analysis of grafted plant samples revealed that the scion genotype highly influences the rootstock microbiome. Under the presented experimental conditions, the rootstock 'Natal Brier' core microbiome consisted of 16 bacterial and 40 fungal taxa. Our results highlight that the scion genotype influences root microbe's recruitment, which might also influence the functionality of assembled microbiomes.}, }
@article {pmid37237476, year = {2023}, author = {Pezzino, S and Sofia, M and Mazzone, C and Castorina, S and Puleo, S and Barchitta, M and Agodi, A and Gallo, L and La Greca, G and Latteri, S}, title = {Gut Microbiome in the Progression of NAFLD, NASH and Cirrhosis, and Its Connection with Biotics: A Bibliometric Study Using Dimensions Scientific Research Database.}, journal = {Biology}, volume = {12}, number = {5}, pages = {}, doi = {10.3390/biology12050662}, pmid = {37237476}, issn = {2079-7737}, abstract = {There is growing evidence that gut microbiota dysbiosis is linked to the etiopathogenesis of nonalcoholic fatty liver disease (NAFLD), from the initial stage of disease until the progressive stage of nonalcoholic steatohepatitis (NASH) and the final stage of cirrhosis. Conversely, probiotics, prebiotics, and synbiotics have shown promise in restoring dysbiosis and lowering clinical indicators of disease in a number of both preclinical and clinical studies. Additionally, postbiotics and parabiotics have recently garnered some attention. The purpose of this bibliometric analysis is to assess recent publishing trends concerning the role of the gut microbiome in the progression of NAFLD, NASH and cirrhosis and its connection with biotics. The free access version of the Dimensions scientific research database was used to find publications in this field from 2002 to 2022. VOSviewer and Dimensions' integrated tools were used to analyze current research trends. Research into the following topics is expected to emerge in this field: (1) evaluation of risk factors which are correlated with the progression of NAFLD, such as obesity and metabolic syndrome; (2) pathogenic mechanisms, such as liver inflammation through toll-like receptors activation, or alteration of short-chain fatty acids metabolisms, which contribute to NAFLD development and its progression in more severe forms, such as cirrhosis; (3) therapy for cirrhosis through dysbiosis reduction, and research on hepatic encephalopathy a common consequence of cirrhosis; (4) evaluation of diversity, and composition of gut microbiome under NAFLD, and as it varies under NASH and cirrhosis by rRNA gene sequencing, a tool which can also be used for the development of new probiotics and explore into the impact of biotics on the gut microbiome; (5) treatments to reduce dysbiosis with new probiotics, such as Akkermansia, or with fecal microbiome transplantation.}, }
@article {pmid37237407, year = {2023}, author = {Schamarek, I and Anders, L and Chakaroun, RM and Kovacs, P and Rohde-Zimmermann, K}, title = {The role of the oral microbiome in obesity and metabolic disease: potential systemic implications and effects on taste perception.}, journal = {Nutrition journal}, volume = {22}, number = {1}, pages = {28}, pmid = {37237407}, issn = {1475-2891}, abstract = {Obesity and its metabolic sequelae still comprise a challenge when it comes to understanding mechanisms, which drive these pandemic diseases. The human microbiome as a potential key player has attracted the attention of broader research for the past decade. Most of it focused on the gut microbiome while the oral microbiome has received less attention. As the second largest niche, the oral microbiome is associated with a multitude of mechanisms, which are potentially involved in the complex etiology of obesity and associated metabolic diseases. These mechanisms include local effects of oral bacteria on taste perception and subsequent food preference as well as systemic effects on adipose tissue function, the gut microbiome and systemic inflammation. This review summarizes a growing body of research, pointing towards a more prominent role of the oral microbiome in obesity and associated metabolic diseases than expected. Ultimately, our knowledge on the oral microbiome may support the development of new patient oriented therapeutic approaches inevitable to relieve the health burden of metabolic diseases and to reach long-term benefits in patients´ lives.}, }
@article {pmid37237381, year = {2023}, author = {Jeon, YJ and Gil, CH and Won, J and Jo, A and Kim, HJ}, title = {Symbiotic microbiome Staphylococcus epidermidis restricts IL-33 production in allergic nasal epithelium via limiting the cellular necroptosis.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {154}, pmid = {37237381}, issn = {1471-2180}, abstract = {BACKGROUND: Allergic rhinitis (AR) is characterized by airway inflammation in nasal mucosa from inhaled allergens and interleukin (IL)-33 is the potent inducer of Th2 inflammation in allergic nasal epithelium. Staphylococcus epidermidis is one of the most abundant colonizers of the healthy human nasal mucosa and might impact the allergen-induced inflammatory responses in the nasal epithelium. Thus, we sought to characterize the mechanism of S. epidermidis regulating Th2 inflammation and IL-33 production in AR nasal mucosa.<br><br>RESULTS: The AR symptoms were alleviated and eosinophilic infiltration, serum IgE levels, and Th2 cytokines were significantly decreased in OVA-sensitized AR mice in response to human nasal commensal S. epidermidis. The inoculation of S. epidermidis to normal human nasal epithelial cells reduced IL-33 and GATA3 transcriptions and also reduced IL-33 and GATA3 expression in AR nasal epithelial (ARNE) cells and the nasal mucosa of AR mice. Our data exhibited that the cellular necroptosis of ARNE cells might be involved in IL-33 production and inoculation of S. epidermidis decreased the phosphorylation of necroptosis enzymes in ARNE cells, which was related to the reduction of IL-33 production.<br><br>CONCLUSIONS: We present that human nasal commensal S. epidermidis reduces allergic inflammation by suppressing IL-33 production in nasal epithelium. Our findings indicate that S. epidermidis serves a role in blocking allergen-induced cellular necroptosis in allergic nasal epithelium which might be a key mechanism of reduction of IL-33 and Th2 inflammation.}, }
@article {pmid37237317, year = {2023}, author = {Coutinho, FH and Silveira, CB and Sebastián, M and Sánchez, P and Duarte, CM and Vaqué, D and Gasol, JM and Acinas, SG}, title = {Water mass age structures the auxiliary metabolic gene content of free-living and particle-attached deep ocean viral communities.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {118}, pmid = {37237317}, issn = {2049-2618}, abstract = {BACKGROUND: Viruses play important roles in the ocean's biogeochemical cycles. Yet, deep ocean viruses are one of the most under-explored fractions of the global biosphere. Little is known about the environmental factors that control the composition and functioning of their communities or how they interact with their free-living or particle-attached microbial hosts.<br><br>RESULTS: We analysed 58 viral communities associated with size-fractionated free-living (0.2-0.8 &#x3bc;m) and particle-attached (0.8-20 &#x3bc;m) cellular metagenomes from bathypelagic (2150-4018 m deep) microbiomes obtained during the Malaspina expedition. These metagenomes yielded 6631 viral sequences, 91% of which were novel, and 67 represented high-quality genomes. Taxonomic classification assigned 53% of the viral sequences to families of tailed viruses from the order Caudovirales. Computational host prediction associated 886 viral sequences to dominant members of the deep ocean microbiome, such as Alphaproteobacteria (284), Gammaproteobacteria (241), SAR324 (23), Marinisomatota (39), and Chloroflexota (61). Free-living and particle-attached viral communities had markedly distinct taxonomic composition, host prevalence, and auxiliary metabolic gene content, which led to the discovery of novel viral-encoded metabolic genes involved in the folate and nucleotide metabolisms. Water mass age emerged as an important factor driving viral community composition. We postulated this was due to changes in quality and concentration of dissolved organic matter acting on the host communities, leading to an increase of viral auxiliary metabolic genes associated with energy metabolism among older water masses.<br><br>CONCLUSIONS: These results shed light on the mechanisms by which environmental gradients of deep ocean ecosystems structure the composition and functioning of free-living and particle-attached viral communities. Video Abstract.}, }
@article {pmid37237024, year = {2023}, author = {Kim, MJ and Park, S and Park, JW and Choi, J and Kim, HJ and Lim, HK and Ryoo, SB and Park, KJ and Ji, Y and Jeong, SY}, title = {Gut microbiome associated with low anterior resection syndrome after rectal cancer surgery.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8578}, pmid = {37237024}, issn = {2045-2322}, abstract = {This study aimed to assess the likely association of gut microbiome with low anterior resection syndrome (LARS) symptoms. Postoperative stool samples from patients with minor or major LARS after sphincter-preserving surgery (SPS) for rectal cancer were collected and analyzed using 16S ribosomal RNA sequencing method. The symptom patterns of LARS were classified into two groups (PC1LARS, PC2LARS) using principal component analysis. The dichotomized sum of questionnaire items (sub1LARS, sub2LARS) was used to group patients according to the main symptoms. According to microbial diversity, enterotype, and taxa, PC1LARS and sub1LARS were associated with frequency-dominant LARS symptoms and patients, while PC2LARS and sub2LARS were grouped as incontinence-dominant LARS symptoms and patients. Butyricicoccus levels decreased while overall LARS scores increased. The α-diversity richness index Chao1 showed a significantly negative correlation in sub1LARS and a positive correlation in sub2LARS. In sub1LARS, the severe group showed a lower Prevotellaceae enterotype and higher Bacteroidaceae enterotype than the mild group. Subdoligranulum and Flavonifractor showed a negative and a positive correlation with PC1LARS, respectively, while showing a negative relationship with PC2LARS. Lactobacillus and Bifidobacterium were negatively correlated to PC1LARS. Frequency-dominant LARS had decreased diversity of gut microbiome and showed lower levels of lactic acid-producing bacteria.}, }
@article {pmid37236960, year = {2023}, author = {Wang, WJ and Yu, LM and Shao, MY and Jia, YT and Liu, LQ and Ma, XH and Zheng, Y and Liu, YF and Zhang, YZ and Luo, XX and Li, FM and Zheng, H}, title = {Research review on the pollution of antibiotic resistance genes in livestock and poultry farming environments.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {34}, number = {5}, pages = {1415-1429}, doi = {10.13287/j.1001-9332.202305.032}, pmid = {37236960}, issn = {1001-9332}, abstract = {Increasingly serious pollution of antibiotic resistance genes (ARGs) caused by the abuse of antibiotics in livestock and poultry industry has raised worldwide concerns. ARGs could spread among various farming environmental media through adsorption, desorption, migration, and also could transfer into human gut microbiome by hori-zontal gene transfer (HGT), posing potential threats to public health. However, the comprehensive review on the pollution patterns, environmental behaviors, and control techniques of ARGs in livestock and poultry environments in view of One Health is still inadequate, resulting in the difficulties in effectively assessing ARGs transmission risk and developing the efficient control strategies. Here, we analyzed the pollution characteristics of typical ARGs in various countries, regions, livestock species, and environmental media, reviewed the critical environmental fate and influencing factors, control strategies, and the shortcomings of current researches about ARGs in the livestock and poultry farming industry combined with One Health philosophy. In particular, we addressed the importance and urgency of identifying the distribution characteristics and environmental process mechanisms of ARGs, and developing green and efficient ARG control means in livestock farming environments. We further proposed gaps and prospects for the future research. It would provide theoretical basis for the research on health risk assessment and technology exploitation of alleviating ARG pollution in livestock farming environment.}, }
@article {pmid37236891, year = {2023}, author = {Graham, DB and Xavier, RJ}, title = {Conditioning of the immune system by the microbiome.}, journal = {Trends in immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.it.2023.05.002}, pmid = {37236891}, issn = {1471-4981}, abstract = {The human intestinal microbiome has coevolved with its host to establish a stable homeostatic relationship with hallmark features of mutualistic symbioses, yet the mechanistic underpinnings of host-microbiome interactions are incompletely understood. Thus, it is an opportune time to conceive a common framework for microbiome-mediated regulation of immune function. We propose the term conditioned immunity to describe the multifaceted mechanisms by which the microbiome modulates immunity. In this regard, microbial colonization is a conditioning exposure that has durable effects on immune function through the action of secondary metabolites, foreign molecular patterns, and antigens. Here, we discuss how spatial niches impact host exposure to microbial products at the level of dose and timing, which elicit diverse conditioned responses.}, }
@article {pmid37236506, year = {2023}, author = {Zilliox, MJ and Bouchard, CS}, title = {The Microbiome, Ocular Surface, and Corneal Disorders.}, journal = {The American journal of pathology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajpath.2023.05.004}, pmid = {37236506}, issn = {1525-2191}, abstract = {The ocular surface microbiome is an emerging field of study that seeks to understand how the community of microorganisms found on the ocular surface may help maintain homeostasis or can potentially lead to disease and dysbiosis. Initial questions include whether the organisms detected on the ocular surface inhabit that ecological niche and, if so, does there exist a "core" microbiome found in most or all healthy eyes. In diseased eyes, many questions have emerged around whether novel organisms and/or a redistribution of organisms play a role in disease pathogenesis, response to therapies or convalescence. Although there is much enthusiasm about this topic, the ocular surface microbiome is a new field with many technical challenges. These challenges are discussed in this review as well as a need for standardization in order to adequately compare studies and advance the field. In addition, this review summarizes the current research on the microbiome of various ocular surface diseases and how these findings may impact treatments and clinical decision-making.}, }
@article {pmid37236111, year = {2023}, author = {Jeong, Y and Vyas, K and Irudayaraj, J}, title = {Toxicity of per- and polyfluoroalkyl substances to microorganisms in confined hydrogel structures.}, journal = {Journal of hazardous materials}, volume = {456}, number = {}, pages = {131672}, doi = {10.1016/j.jhazmat.2023.131672}, pmid = {37236111}, issn = {1873-3336}, abstract = {Per- and polyfluoroalkyl substances (PFAS) as a group of environmentally persistent synthetic chemicals has been widely used in industrial and consumer products. Bioaccumulation studies have documented the adverse effects of PFAS in various living organisms. Despite the large number of studies, experimental approaches to evaluate the toxicity of PFAS on bacteria in a biofilm-like niche as structured microbial communities are sparse. This study suggests a facile approach to query the toxicity of PFOS and PFOA on bacteria (Escherichia coli K12 MG1655 strain) in a biofilm-like niche provided by hydrogel-based core-shell beads. Our study shows that E. coli MG1655 upon complete confinement in hydrogel beads exhibit altered physiological characteristics of viability, biomass, and protein expression, compared to their susceptible counterpart cultivated under planktonic conditions. We find that soft-hydrogel engineering platforms may provide a protective role for microorganisms from environmental contaminants, depending on the size or thickness of the protective/barrier layer. We expect our study to provide insights on the toxicity of environmental contaminants on organisms under encapsulated conditions that could potentially be useful for toxicity screening and in evaluating ecological risk of soil, plant, and mammalian microbiome.}, }
@article {pmid37235836, year = {2023}, author = {Rashidi, A and Ebadi, M and Rehman, TU and Elhusseini, H and Kazadi, D and Halaweish, H and Khan, MH and Hoeschen, A and Cao, Q and Luo, X and Kabage, AJ and Lopez, S and Holtan, SG and Weisdorf, DJ and Khoruts, A and Staley, C}, title = {Randomized Double-Blind Phase II Trial of Fecal Microbiota Transplantation Versus Placebo in Allogeneic Hematopoietic Cell Transplantation and AML.}, journal = {Journal of clinical oncology : official journal of the American Society of Clinical Oncology}, volume = {}, number = {}, pages = {JCO2202366}, doi = {10.1200/JCO.22.02366}, pmid = {37235836}, issn = {1527-7755}, abstract = {PURPOSE: Gut microbiota injury in allogeneic hematopoietic cell transplantation (HCT) recipients and patients with AML has been associated with adverse clinical outcomes. Previous studies in these patients have shown improvements in various microbiome indices after fecal microbiota transplantation (FMT). However, whether microbiome improvements translate into improved clinical outcomes remains unclear. We examined this question in a randomized, double-blind, placebo-controlled phase II trial.<br><br>METHODS: Two independent cohorts of allogeneic HCT recipients and patients with AML receiving induction chemotherapy were randomly assigned in a 2:1 ratio to receive standardized oral encapsulated FMT versus placebo upon neutrophil recovery. After each course of antibacterial antibiotics, patients received a study treatment. Up to three treatments were administered within 3 months. The primary end point was 4-month all-cause infection rate. Patients were followed for 9 months.<br><br>RESULTS: In the HCT cohort (74 patients), 4-month infection density was 0.74 and 0.91 events per 100 patient-days in FMT and placebo arms, respectively (infection rate ratio, 0.83; 95% CI, 0.48 to 1.42; P = .49). In the AML cohort (26 patients), 4-month infection density was 0.93 in the FMT arm and 1.25 in the placebo arm, with an infection rate ratio of 0.74 (95% CI, 0.32 to 1.71; P = .48). Unique donor bacterial sequences comprised 25%-30% of the fecal microbiota after FMT. FMT improved postantibiotic recovery of microbiota diversity, restored several depleted obligate anaerobic commensals, and reduced the abundance of expanded genera Enterococcus, Streptococcus, Veillonella, and Dialister.<br><br>CONCLUSION: In allogeneic HCT recipients and patients with AML, third-party FMT was safe and ameliorated intestinal dysbiosis, but did not decrease infections. Novel findings from this trial will inform future development of FMT trials.}, }
@article {pmid37235662, year = {2023}, author = {He, H and Qin, Q and Xu, F and Chen, Y and Rao, S and Wang, C and Jiang, X and Lu, X and Xie, C}, title = {Oral polyphenol-armored nanomedicine for targeted modulation of gut microbiota-brain interactions in colitis.}, journal = {Science advances}, volume = {9}, number = {21}, pages = {eadf3887}, doi = {10.1126/sciadv.adf3887}, pmid = {37235662}, issn = {2375-2548}, abstract = {Developing oral nanomedicines that suppress intestinal inflammation while modulating gut microbiota and brain interactions is essential for effectively treating inflammatory bowel disease. Here, we report an oral polyphenol-armored nanomedicine based on tumor necrosis factor-α (TNF-α)-small interfering RNA and gallic acid-mediated graphene quantum dot (GAGQD)-encapsulated bovine serum albumin nanoparticle, with a chitosan and tannin acid (CHI/TA) multilayer. Referred to "armor," the CHI/TA multilayer resists the harsh environment of the gastrointestinal tract and adheres to inflamed colon sites in a targeted manner. TA provides antioxidative stress and prebiotic activities that modulate the diverse gut microbiota. Moreover, GAGQD protected TNF-α-siRNA delivery. Unexpectedly, the armored nanomedicine suppressed hyperactive immune responses and modulated bacterial gut microbiota homeostasis in a mouse model of acute colitis. Notably, the armored nanomedicine alleviated anxiety- and depression-like behaviors and cognitive impairment in mice with colitis. This armor strategy sheds light on the effect of oral nanomedicines on bacterial gut microbiome-brain interactions.}, }
@article {pmid37235629, year = {2023}, author = {Kim, BG and Kang, N and Kim, SY and Kim, DH and Kim, H and Kwon, OJ and Huh, HJ and Lee, NY and Jhun, BW}, title = {The lung microbiota in nontuberculous mycobacterial pulmonary disease.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0285143}, pmid = {37235629}, issn = {1932-6203}, abstract = {BACKGROUND: The role of bacterial microbiota in the pathogenesis of nontuberculous mycobacterial pulmonary disease (NTM-PD) is unclear. We aimed to compare the bacterial microbiome of disease-invaded lesions and non-invaded lung tissue from NTM-PD patients.<br><br>METHODS: We analyzed lung tissues from 23 NTM-PD patients who underwent surgical lung resection. Lung tissues were collected in pairs from each patient, with one sample from a disease-involved site and the other from a non-involved site. Lung tissue microbiome libraries were constructed using 16S rRNA gene sequences (V3-V4 regions).<br><br>RESULTS: Sixteen (70%) patients had Mycobacterium avium complex (MAC)-PD, and the remaining seven (30%) had Mycobacterium abscessus-PD. Compared to non-involved sites, involved sites showed greater species richness (ACE, Chao1, and Jackknife analyses, all p = 0.001); greater diversity on the Shannon index (p = 0.007); and genus-level differences (Jensen-Shannon, PERMANOVA p = 0.001). Analysis of taxonomic biomarkers using linear discriminant analysis (LDA) effect sizes (LEfSe) demonstrated that several genera, including Limnohabitans, Rahnella, Lachnospira, Flavobacterium, Megamonas, Gaiella, Subdoligranulum, Rheinheimera, Dorea, Collinsella, and Phascolarctobacterium, had significantly greater abundance in involved sites (LDA >3.00, p <0.05, and q <0.05). In contrast, Acinetobacter had significantly greater abundance at non-involved sites (LDA = 4.27, p<0.001, and q = 0.002). Several genera were differentially distributed between lung tissues from MAC-PD (n = 16) and M. abscessus-PD (n = 7), and between nodular bronchiectatic form (n = 12) and fibrocavitary form (n = 11) patients. However, there was no genus with a significant q-value.<br><br>CONCLUSIONS: We identified differential microbial distributions between disease-invaded and normal lung tissues from NTM-PD patients, and microbial diversity was significantly higher in disease-invaded tissues.<br><br>TRIAL REGISTRATION: Clinical Trial registration number: NCT00970801.}, }
@article {pmid37235511, year = {2023}, author = {Vorobyev, A and Ludwig, RJ}, title = {Research in practice: Diet and microbiome in autoimmune diseases.}, journal = {Journal der Deutschen Dermatologischen Gesellschaft = Journal of the German Society of Dermatology : JDDG}, volume = {}, number = {}, pages = {}, doi = {10.1111/ddg.15101}, pmid = {37235511}, issn = {1610-0387}, abstract = {The incidence of autoimmune diseases in industrialized countries is constantly increasing over past decades. These diseases lead to increased mortality and persistent reduction in quality of life of the patients, posing a severe medical burden. Treatment of autoimmune diseases is often based on unspecific immune suppression, increasing the risk of infectious diseases as well as cancer manifestation. Pathogenesis of autoimmune conditions is complex and includes not only genetic factors, but also environmental influence, which is considered to be the reason for the rise of incidence of autoimmune diseases. Environmental factors comprise numerous elements, such as infections, smoking, medication, diet etc., which can either promote or prevent the onset of autoimmunity. However, the mechanisms of environmental influence are complex and for this moment not clearly understood. Deciphering of these interactions could enhance our comprehension of autoimmunity and provide some novel treatment options for the patients.}, }
@article {pmid37235443, year = {2023}, author = {Ko, YS and Tark, D and Moon, SH and Kim, DM and Lee, TG and Bae, DY and Sunwoo, SY and Oh, Y and Cho, HS}, title = {Alteration of the Gut Microbiota in Pigs Infected with African Swine Fever Virus.}, journal = {Veterinary sciences}, volume = {10}, number = {5}, pages = {}, doi = {10.3390/vetsci10050360}, pmid = {37235443}, issn = {2306-7381}, abstract = {The factors that influence the pathogenicity of African swine fever (ASF) are still poorly understood, and the host's immune response has been indicated as crucial. Although an increasing number of studies have shown that gut microbiota can control the progression of diseases caused by viral infections, it has not been characterized how the ASF virus (ASFV) changes a pig's gut microbiome. This study analyzed the dynamic changes in the intestinal microbiome of pigs experimentally infected with the high-virulence ASFV genotype II strain (N = 4) or mock strain (N = 3). Daily fecal samples were collected from the pigs and distributed into the four phases (before infection, primary phase, clinical phase, and terminal phase) of ASF based on the individual clinical features of the pigs. The total DNA was extracted and the V4 region of the 16 s rRNA gene was amplified and sequenced on the Illumina platform. Richness indices (ACE and Chao1) were significantly decreased in the terminal phase of ASF infection. The relative abundances of short-chain-fatty-acids-producing bacteria, such as Ruminococcaceae, Roseburia, and Blautia, were decreased during ASFV infection. On the other hand, the abundance of Proteobacteria and Spirochaetes increased. Furthermore, predicted functional analysis using PICRUSt resulted in a significantly reduced abundance of 15 immune-related pathways in the ASFV-infected pigs. This study provides evidence for further understanding the ASFV-pig interaction and suggests that changes in gut microbiome composition during ASFV infection may be associated with the status of immunosuppression.}, }
@article {pmid37235414, year = {2023}, author = {Banchi, P and Colitti, B and Del Carro, A and Corrò, M and Bertero, A and Ala, U and Del Carro, A and Van Soom, A and Bertolotti, L and Rota, A}, title = {Challenging the Hypothesis of in Utero Microbiota Acquisition in Healthy Canine and Feline Pregnancies at Term: Preliminary Data.}, journal = {Veterinary sciences}, volume = {10}, number = {5}, pages = {}, doi = {10.3390/vetsci10050331}, pmid = {37235414}, issn = {2306-7381}, abstract = {At present, there are no data on the presence of bacteria in healthy canine and feline pregnancies at term. Here, we investigated the uterine microbiome in bitches (n = 5) and queens (n = 3) undergoing elective cesarean section in two facilities. Samples included swabs from the endometrium, amniotic fluid, and meconium, and environmental swabs of the surgical tray as controls. Culture and 16S rRNA gene sequencing were used to investigate the presence of bacteria. Culture was positive for 34.3% of samples (uterus n = 3, amniotic fluid n = 2, meconium n = 4, controls n = 0), mostly with low growth of common contaminant bacteria. With sequencing techniques, the bacterial abundance was significantly lower than in environmental controls (p < 0.05). Sequencing results showed a species-specific pattern, and significant differences between canine and feline bacterial populations were found at order, family, and genus level. No differences were found in alpha and beta diversities between feto-maternal tissues and controls (p > 0.05). Dominant phyla were Bacteroidetes, Firmicutes, and Proteobacteria in different proportions based on tissue and species. Culture and sequencing results suggest that the bacterial biomass is very low in healthy canine and feline pregnancies at term, that bacteria likely originate from contamination from the dam's skin, and that the presence of viable bacteria could not be confirmed most of the time.}, }
@article {pmid37235272, year = {2023}, author = {Li, J and Chen, X and Zhao, S and Chen, J}, title = {Arsenic-Containing Medicine Treatment Disturbed the Human Intestinal Microbial Flora.}, journal = {Toxics}, volume = {11}, number = {5}, pages = {}, doi = {10.3390/toxics11050458}, pmid = {37235272}, issn = {2305-6304}, abstract = {Human intestinal microbiome plays vital role in maintaining intestinal homeostasis and interacting with xenobiotics. Few investigations have been conducted to understand the effect of arsenic-containing medicine exposure on gut microbiome. Most animal experiments are onerous in terms of time and resources and not in line with the international effort to reduce animal experiments. We explored the overall microbial flora by 16S rRNA genes analysis in fecal samples from acute promyelocytic leukemia (APL) patients treated with arsenic trioxide (ATO) plus all-trans retinoic acid (ATRA). Gut microbiomes were found to be overwhelmingly dominated by Firmicutes and Bacteroidetes after taking medicines containing arsenic in APL patients. The fecal microbiota composition of APL patients after treatment showed lower diversity and uniformity shown by the alpha diversity indices of Chao, Shannon, and Simpson. Gut microbiome operational taxonomic unit (OTU) numbers were associated with arsenic in the feces. We evaluated Bifidobacterium adolescentis and Lactobacillus mucosae to be a keystone in APL patients after treatment. Bacteroides at phylum or genus taxonomic levels were consistently affected after treatment. In the most common gut bacteria Bacteroides fragilis, arsenic resistance genes were significantly induced by arsenic exposure in anaerobic pure culture experiments. Without an animal model, without taking arsenicals passively, the results evidence that arsenic exposure by drug treatment is not only associated with alterations in intestinal microbiome development at the abundance and diversity level, but also induced arsenic biotransformation genes (ABGs) at the function levels which may even extend to arsenic-related health outcomes in APL.}, }
@article {pmid37235163, year = {2023}, author = {Safika, S and Indrawati, A and Afiff, U and Hastuti, YT and Zureni, Z and Jati, AP}, title = {First Study on profiling of gut microbiome in wild and captive Sumatran orangutans (Pongo abelii).}, journal = {Veterinary world}, volume = {16}, number = {4}, pages = {717-727}, pmid = {37235163}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: Orangutans are an "umbrella species" for conserving tropical forests in Sumatra and Kalimantan. There are remarkable changes between the gut microbiomes of wild and captive Sumatran orangutans. This study aimed to profile gut microbiota of wild and captive Sumatran orangutans.<br><br>MATERIALS AND METHODS: Nine fecal samples collected from wild orangutans and nine fecal samples collected from captive orangutans were divided into three replicates. Each replicate randomly combined three pieces and were analyzed on the Illumina platform. A bioinformatics study of 16S rRNA according to Qiime2 (Version 2021.4) and microbiome profiling analysis was conducted.<br><br>RESULTS: The relative abundance of different microbial taxa varied significantly between wild and captive Sumatran orangutans. Among the operational taxonomic units, various proportions of Firmicutes, Proteobacteria, Bacteroidetes, Euryarchaeota, Acidobacteria, Actinobacteria and Verrucomicrobia predominated. Solobacterium was found only in 19% of captive orangutans. Methanobrevibacter was identified to be prevalent among wild orangutans (16%). Analysis of the core microbiome from the combined wild and captive data revealed seven species as cores. According to linear discriminant analysis effect size, Micrococcus luteus, Bacteroidescaccae, Lachnospiraceae bacterium, Ruthenibacterium lactatiformans, Haemophilus haemolyticus, and Chishuiella spp. were microbiome biomarkers in captive orangutans, whereas Roseburia inulinivorans, Collinsella aerofaciens, Oscillibacter spp., and Eubacterium hallii were microbiome biomarkers in wild orangutans.<br><br>CONCLUSION: There were differences in the microbiome biomarkers of wild and captive Sumatran orangutans. This study is important for understanding the role of gut bacteria in the health of Sumatran orangutans.}, }
@article {pmid37235073, year = {2023}, author = {Nagarakanti, S and Orenstein, R}, title = {Treating Clostridioides difficile: Could Microbiota-based Live Biotherapeutic Products Provide the Answer?.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {3137-3143}, pmid = {37235073}, issn = {1178-6973}, abstract = {Clostridioides difficile infection (CDI) is a pressing health care issue due to the limited effectiveness of current treatments and high recurrence rates. Current available antibiotic options for CDI disrupt the fecal microbiome which predisposes recurrent CDI. Fecal microbiota transplantation (FMT) has improved the outcomes of recurrent CDI, but concerns surrounding the safety and standardization of the product persist. Microbiota-based live biotherapeutic products (LBPs), are emerging as potential alternatives to FMT for CDI treatment. This review explores the potential of LBPs as safe and effective therapy for CDI. While preclinical and early clinical studies have shown promising results, further research is necessary to determine the optimal composition and dosage of LBPs and to ensure their safety and efficacy in clinical practice. Overall, LBPs hold great promise as a novel therapy for CDI and warrant further investigation in other conditions related to disruption of the colonic microbiota.}, }
@article {pmid37235047, year = {2023}, author = {Borbet, TC and Pawline, MB and Li, J and Ho, ML and Yin, YS and Zhang, X and Novikova, E and Jackson, K and Mullins, BJ and Ruiz, VE and Hines, MJ and Zhang, XS and Müller, A and Koralov, SB and Blaser, MJ}, title = {Disruption of the early-life microbiota alters Peyer's patch development and germinal center formation in gastrointestinal-associated lymphoid tissue.}, journal = {iScience}, volume = {26}, number = {6}, pages = {106810}, doi = {10.1016/j.isci.2023.106810}, pmid = {37235047}, issn = {2589-0042}, abstract = {During postnatal development, both the maturing microbiome and the host immune system are susceptible to environmental perturbations such as antibiotic use. The impact of timing in which antibiotic exposure occurs was investigated by treating mice from days 5-9 with amoxicillin or azithromycin, two of the most commonly prescribed medications in children. Both early-life antibiotic regimens disrupted Peyer's patch development and immune cell abundance, with a sustained decrease in germinal center formation and diminished intestinal immunoglobulin A (IgA) production. These effects were less pronounced in adult mice. Through comparative analysis of microbial taxa, Bifidobacterium longum abundance was found to be associated with germinal center frequency. When re-introduced to antibiotic-exposed mice, B. longum partially rescued the immunological deficits. These findings suggest that early-life antibiotic use affects the development of intestinal IgA-producing B cell functions and that probiotic strains could be used to restore normal development after antibiotic exposure.}, }
@article {pmid37234911, year = {2023}, author = {Holm, JB and Carter, KA and Ravel, J and Brotman, RM}, title = {Lactobacillus iners and genital health: molecular clues to an enigmatic vaginal species.}, journal = {Current infectious disease reports}, volume = {25}, number = {4}, pages = {67-75}, doi = {10.1007/s11908-023-00798-5}, pmid = {37234911}, issn = {1523-3847}, abstract = {PURPOSE OF REVIEW: Vaginal lactobacilli are recognized as important drivers of genital health including protection against bacterial vaginosis and sexually transmitted infections. Lactobacillus iners is distinct from L. crispatus, L. gasseri, and L. jensenii by its high global prevalence in vaginal microbiomes, relatively small genome, production of only L-lactic acid, and inconsistent associations with genital health outcomes. In this review, we summarize our current understanding of the role of L. iners in the vaginal microbiome, highlight the importance of strain-level consideration for this species, and explain that while marker gene-based characterization of the composition of the vaginal microbiota does not capture strain-level resolution, whole metagenome sequencing can aid in expanding our understanding of this species in genital health.<br><br>RECENT FINDINGS: L. iners exists in the vaginal microbiome as a unique combination of strains. The functional repertoires of these strain combinations are likely wide and contribute to the survival of this species in a variety of vaginal microenvironments. In published studies to date, strain-specific effects are aggregated and may yield imprecise estimates of risk associated with this species.<br><br>SUMMARY: The worldwide high prevalence of Lactobacillus iners warrants more research into its functional roles in the vaginal microbiome and how it may directly impact susceptibility to infections. By incorporating strain-level resolution into future research endeavors, we may begin to appreciate L. iners more thoroughly and identify novel therapeutic targets for a variety of genital health challenges.}, }
@article {pmid37234898, year = {2023}, author = {Kaur, A and Lin, W and Dovhalyuk, V and Driutti, L and Di Martino, ML and Vujasinovic, M and Löhr, JM and Sellin, ME and Globisch, D}, title = {Chemoselective bicyclobutane-based mass spectrometric detection of biological thiols uncovers human and bacterial metabolites.}, journal = {Chemical science}, volume = {14}, number = {20}, pages = {5291-5301}, doi = {10.1039/d3sc00224a}, pmid = {37234898}, issn = {2041-6520}, abstract = {Sulfur is an essential element of life. Thiol-containing metabolites in all organisms are involved in the regulation of diverse biological processes. Especially, the microbiome produces bioactive metabolites or biological intermediates of this compound class. The analysis of thiol-containing metabolites is challenging due to the lack of specific tools, making these compounds difficult to investigate selectively. We have now developed a new methodology comprising bicyclobutane for chemoselective and irreversible capturing of this metabolite class. We utilized this new chemical biology tool immobilized onto magnetic beads for the investigation of human plasma, fecal samples, and bacterial cultures. Our mass spectrometric investigation detected a broad range of human, dietary and bacterial thiol-containing metabolites and we even captured the reactive sulfur species cysteine persulfide in both fecal and bacterial samples. The described comprehensive methodology represents a new mass spectrometric strategy for the discovery of bioactive thiol-containing metabolites in humans and the microbiome.}, }
@article {pmid37234762, year = {2023}, author = {Dixon, M and Dunlop, AL and Corwin, EJ and Kramer, MR}, title = {Corrigendum: Joint effects of individual socioeconomic status and residential neighborhood context on vaginal microbiome composition.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1192743}, doi = {10.3389/fpubh.2023.1192743}, pmid = {37234762}, issn = {2296-2565}, abstract = {[This corrects the article DOI: 10.3389/fpubh.2023.1029741.].}, }
@article {pmid37234705, year = {2023}, author = {Zou, Y and Sun, Y and Chen, X and Hong, L and Dong, G and Bai, X and Wang, H and Rao, B and Ren, Z and Yu, Z}, title = {Nanosecond pulse effectively ablated hepatocellular carcinoma with alterations in the gut microbiome and serum metabolites.}, journal = {Frontiers in pharmacology}, volume = {14}, number = {}, pages = {1163628}, doi = {10.3389/fphar.2023.1163628}, pmid = {37234705}, issn = {1663-9812}, abstract = {Background: Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death in the world. Nanosecond pulsed electric fields (nsPEFs) have emerged as a new treatment for cancer. This study aims to identify the effectiveness of nsPEFs in the treatment of HCC and analyze the alterations in the gut microbiome and serum metabonomics after ablation. Methods: C57BL/6 mice were randomly divided into three groups: healthy control mice (n = 10), HCC mice (n = 10), and nsPEF-treated HCC mice (n = 23). Hep1-6 cell lines were used to establish the HCC model in situ. Histopathological staining was performed on tumor tissues. The gut microbiome was analyzed by 16S rRNA sequencing. Serum metabolites were analyzed by liquid chromatography-mass spectrometry (LC-MS) metabolomic analysis. Spearman's correlation analysis was carried out to analyze the correlation between the gut microbiome and serum metabonomics. Results: The fluorescence image showed that nsPEFs were significantly effective. Histopathological staining identified nuclear pyknosis and cell necrosis in the nsPEF group. The expression of CD34, PCNA, and VEGF decreased significantly in the nsPEF group. Compared with normal mice, the gut microbiome diversity of HCC mice was increased. Eight genera including Alistipes and Muribaculaceae were enriched in the HCC group. Inversely, these genera decreased in the nsPEF group. LC-MS analysis confirmed that there were significant differences in serum metabolism among the three groups. Correlation analysis showed crucial relationships between the gut microbiome and serum metabolites that are involved in nsPEF ablation of HCC. Conclusion: As a new minimally invasive treatment for tumor ablation, nsPEFs have an excellent ablation effect. The alterations in the gut microbiome and serum metabolites may participate in the prognosis of HCC ablation.}, }
@article {pmid37234541, year = {2023}, author = {Chen, P and Zhang, G and Wang, J}, title = {Editorial: Cancer diagnosis and novel drug discovery based on microbiome.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1144986}, doi = {10.3389/fmicb.2023.1144986}, pmid = {37234541}, issn = {1664-302X}, }
@article {pmid37234540, year = {2023}, author = {, }, title = {Erratum: Ksak: a high-throughput tool for alignment-free phylogenetics.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1212612}, doi = {10.3389/fmicb.2023.1212612}, pmid = {37234540}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2023.1050130.].}, }
@article {pmid37234536, year = {2023}, author = {Wang, Z and Kumar, A and Singh, P and Solanki, MK}, title = {Editorial: Actinobacteria plant interaction: recent molecular tools and biology.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1209699}, doi = {10.3389/fmicb.2023.1209699}, pmid = {37234536}, issn = {1664-302X}, }
@article {pmid37234511, year = {2023}, author = {Onallah, H and Hazan, R and Nir-Paz, R and , }, title = {Compassionate Use of Bacteriophages for Failed Persistent Infections During the First 5 Years of the Israeli Phage Therapy Center.}, journal = {Open forum infectious diseases}, volume = {10}, number = {5}, pages = {ofad221}, doi = {10.1093/ofid/ofad221}, pmid = {37234511}, issn = {2328-8957}, abstract = {The use of bacteriophages (phages) is reemerging as a potential treatment option for antibiotic-resistant or nonresolving bacterial infections. Phages are bacteria-specific viruses that may serve as a personalized therapeutic option with minimal collateral damage to the patient or the microbiome. In 2018 we established the Israeli Phage Therapy Center (IPTC) as a shared initiative of the Hadassah Medical Center and the Hebrew University of Jerusalem, aiming to conduct all of the steps required for phage-based solutions, from phage isolation and characterization to treatments, for nonresolving bacterial infections. So far, a total of 159 requests for phage therapy arrived to the IPTC; 145 of them were from Israel and the rest from other countries. This number of registered requests is growing annually. Multidrug-resistant bacteria accounted for 38% of all phage requests. Respiratory and bone infections were the most prevalent among clinical indications and accounted for 51% of the requests. To date, 20 phage therapy courses were given to 18 patients by the IPTC. In 77.7% (n = 14) of the cases, a favorable clinical outcome of infection remission or recovery was seen. Clearly, establishing an Israeli phage center has led to an increased demand for compassionate use of phages with favorable outcomes for many previously failed infections. As clinical trials are still lacking, publishing patient data from cohort studies is pertinent to establish clinical indications, protocols, and success and failure rates. Last, workflow processes and bottlenecks should be shared to enable faster availability and authorization of phages for clinical use.}, }
@article {pmid37234090, year = {2023}, author = {Zhu, X and Yang, P and Xiong, G and Wei, H and Zhang, L and Wang, Z and Ning, K}, title = {Microbial biogeochemical cycling reveals the sustainability of the rice-crayfish co-culture model.}, journal = {iScience}, volume = {26}, number = {5}, pages = {106769}, doi = {10.1016/j.isci.2023.106769}, pmid = {37234090}, issn = {2589-0042}, abstract = {Aquaculture has great potential in nourishing the global growing population, while such staggering yields are coupled with environmental pollution. Rice-crayfish co-culture models (RCFP) have been widely adopted in China due to their eco-friendliness. However, little is known about RCFP's microbiome pattern, which hinders our understanding of its sustainability. This study has conducted metagenomic analysis across aquaculture models and habitats, which revealed aquaculture model-specific biogeochemical cycling pattern (e.g., nitrogen (N), sulfur (S), and carbon (C)): RCFP is advantageous in N-assimilation, N-contamination, and S-pollutants removal, while non-RCFP features N denitrification process and higher S metabolism ability, producing several hazardous pollutants in non-RCFP (e.g., nitric oxide, nitrogen monoxide, and sulfide). Moreover, RCFP has greater capacity for carbohydrate enzyme metabolism compared with non-RCFP in environmental habitats, but not in crayfish gut. Collectively, RCFP plays an indispensable role in balancing aquaculture productivity and environmental protection, which might be applied to the blue transformation of aquaculture.}, }
@article {pmid37233812, year = {2023}, author = {Smalla, K and Kabisch, J and Fiedler, G and Hammerl, JA and Tenhagen, BA}, title = {[Health risks from crop irrigation with treated wastewater containing antibiotic residues, resistance genes, and resistant microorganisms].}, journal = {Bundesgesundheitsblatt, Gesundheitsforschung, Gesundheitsschutz}, volume = {}, number = {}, pages = {}, pmid = {37233812}, issn = {1437-1588}, abstract = {This review describes the effects and potential health risks of resistant microorganisms, resistance genes, and residues of drugs and biocides that occur when re-using wastewater for crop irrigation. It focusses on specific aspects of these contaminants and their interactions, but does not provide a general risk assessment of the microbial load when using reclaimed water.Antimicrobial residues, antimicrobial resistant microorganisms, and resistance genes are frequently detected in treated wastewater. They have effects on the soil and plant-associated microbiota (total associated microorganisms) and can be taken up by plants. An interaction of residues with microorganisms is mainly expected before using the water for irrigation. However, it may also occur as a combined effect on the plant microbiome and all the abundant resistance genes (resistome). Special concerns are raised as plants are frequently consumed raw, that is, without processing that might reduce the bacterial load. Washing fruits and vegetables only has minor effects on the plant microbiome. On the other hand, cutting and other processes may support growth of microorganisms. Therefore, after such process steps, cooling of the foods is required.Further progress has to be made in the treatment of wastewater that will be used for crop irrigation with respect to removing micropollutants and microorganisms to minimize the risk of an increased exposure of consumers to transferable resistance genes and resistant bacteria.}, }
@article {pmid37233803, year = {2023}, author = {Leonhardt, F and Keller, A and Arranz Aveces, C and Ernst, R}, title = {From Alien Species to Alien Communities: Host- and Habitat-Associated Microbiomes in an Alien Amphibian.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37233803}, issn = {1432-184X}, abstract = {Alien species can host diverse microbial communities. These associated microbiomes may be important in the invasion process and their analysis requires a holistic community-based approach. We analysed the skin and gut microbiome of Eleutherodactylus johnstonei from native range populations in St Lucia and exotic range populations in Guadeloupe, Colombia, and European greenhouses along with their respective environmental microbial reservoir through a 16S metabarcoding approach. We show that amphibian-associated and environmental microbial communities can be considered as meta-communities that interact in the assembly process. High proportions of bacteria can disperse between frogs and environment, while respective abundances are rather determined by niche effects driven by the microbial community source and spatial environmental properties. Environmental transmissions appeared to have higher relevance for skin than for gut microbiome composition and variation. We encourage further experimental studies to assess the implications of turnover in amphibian-associated microbial communities and potentially invasive microbiota in the context of invasion success and impacts. Within this novel framework of "nested invasions," (meta-)community ecology thinking can complement and widen the traditional perspective on biological invasions.}, }
@article {pmid37233715, year = {2023}, author = {Mousa, S and Sarfraz, M and Mousa, WK}, title = {The Interplay between Gut Microbiota and Oral Medications and Its Impact on Advancing Precision Medicine.}, journal = {Metabolites}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/metabo13050674}, pmid = {37233715}, issn = {2218-1989}, abstract = {Trillions of diverse microbes reside in the gut and are deeply interwoven with the human physiological process, from food digestion, immune system maturation, and fighting invading pathogens, to drug metabolism. Microbial drug metabolism has a profound impact on drug absorption, bioavailability, stability, efficacy, and toxicity. However, our knowledge of specific gut microbial strains, and their genes that encode enzymes involved in the metabolism, is limited. The microbiome encodes over 3 million unique genes contributing to a huge enzymatic capacity, vastly expanding the traditional drug metabolic reactions that occur in the liver, manipulating their pharmacological effect, and, ultimately, leading to variation in drug response. For example, the microbial deactivation of anticancer drugs such as gemcitabine can lead to resistance to chemotherapeutics or the crucial role of microbes in modulating the efficacy of the anticancer drug, cyclophosphamide. On the other hand, recent findings show that many drugs can shape the composition, function, and gene expression of the gut microbial community, making it harder to predict the outcome of drug-microbiota interactions. In this review, we discuss the recent understanding of the multidirectional interaction between the host, oral medications, and gut microbiota, using traditional and machine-learning approaches. We analyze gaps, challenges, and future promises of personalized medicine that consider gut microbes as a crucial player in drug metabolism. This consideration will enable the development of personalized therapeutic regimes with an improved outcome, ultimately leading to precision medicine.}, }
@article {pmid37233701, year = {2023}, author = {Weninger, SN and Ding, A and Browne, EN and Frost, ML and Schiro, G and Laubitz, D and Duca, FA}, title = {Longitudinal Characterization of the Gut Microbiota in the Diabetic ZDSD Rat Model and Therapeutic Potential of Oligofructose.}, journal = {Metabolites}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/metabo13050660}, pmid = {37233701}, issn = {2218-1989}, support = {R01ES033993/DK/NIDDK NIH HHS/United States ; }, abstract = {The complex development of type 2 diabetes (T2D) creates challenges for studying the progression and treatment of the disease in animal models. A newly developed rat model of diabetes, the Zucker Diabetic Sprague Dawley (ZDSD) rat, closely parallels the progression of T2D in humans. Here, we examine the progression of T2D and associated changes in the gut microbiota in male ZDSD rats and test whether the model can be used to examine the efficacy of potential therapeutics such as prebiotics, specifically oligofructose, that target the gut microbiota. Bodyweight, adiposity, and fed/fasting blood glucose and insulin were recorded over the course of the study. Glucose and insulin tolerance tests were performed, and feces collected at 8, 16, and 24 weeks of age for short-chain fatty acids and microbiota analysis using 16s rRNA gene sequencing. At the end of 24 weeks of age, half of the rats were supplemented with 10% oligofructose and tests were repeated. We observed a transition from healthy/nondiabetic to prediabetic and overtly diabetic states, via worsened insulin and glucose tolerance and significant increases in fed/fasted glucose, followed by a significant decrease in circulating insulin. Acetate and propionate levels were significantly increased in the overt diabetic state compared to healthy and prediabetic. Microbiota analysis demonstrated alterations in the gut microbiota with shifts in alpha and beta diversity as well as alterations in specific bacterial genera in healthy compared to prediabetic and diabetic states. Oligofructose treatment improved glucose tolerance and shifted the cecal microbiota of the ZDSD rats during late-stage diabetes. These findings underscore the translational potential of ZDSD rats as a model of T2D and highlight potential gut bacteria that could impact the development of the disease or serve as a biomarker for T2D. Additionally, oligofructose treatment was able to moderately improve glucose homeostasis.}, }
@article {pmid37233633, year = {2023}, author = {Taş, E and Ülgen, KO}, title = {Understanding the ADHD-Gut Axis by Metabolic Network Analysis.}, journal = {Metabolites}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/metabo13050592}, pmid = {37233633}, issn = {2218-1989}, abstract = {Attention deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder diagnosed with hyperactivity, impulsivity, and a lack of attention inconsistent with the patient's development level. The fact that people with ADHD frequently experience gastrointestinal (GI) dysfunction highlights the possibility that the gut microbiome may play a role in this condition. The proposed research aims to determine a biomarker for ADHD by reconstructing a model of the gut-microbial community. Genome-scale metabolic models (GEM) considering the relationship between gene-protein-reaction associations are used to simulate metabolic activities in organisms of gut. The production rates of dopamine and serotonin precursors and the key short chain fatty acids which affect the health status are determined under three diets (Western, Atkins', Vegan) and compared with those of healthy people. Elasticities are calculated to understand the sensitivity of exchange fluxes to changes in diet and bacterial abundance at the species level. The presence of Bacillota (genus Coprococcus and Subdoligranulum), Actinobacteria (genus Collinsella), Bacteroidetes (genus Bacteroides), and Bacteroidota (genus Alistipes) may be possible gut microbiota indicators of ADHD. This type of modeling approach taking microbial genome-environment interactions into account helps us understand the gastrointestinal mechanisms behind ADHD, and establish a path to improve the quality of life of ADHD patients.}, }
@article {pmid37233297, year = {2023}, author = {Tejeda-Garibay, S and Hoyer, KK}, title = {Coccidioidomycosis and Host Microbiome Interactions: What We Know and What We Can Infer from Other Respiratory Infections.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {5}, pages = {}, doi = {10.3390/jof9050586}, pmid = {37233297}, issn = {2309-608X}, abstract = {Between 70 and 80% of Valley fever patients receive one or more rounds of antibiotic treatment prior to accurate diagnosis with coccidioidomycosis. Antibiotic treatment and infection (bacterial, viral, fungal, parasitic) often have negative implications on host microbial dysbiosis, immunological responses, and disease outcome. These perturbations have focused on the impact of gut dysbiosis on pulmonary disease instead of the implications of direct lung dysbiosis. However, recent work highlights a need to establish the direct effects of the lung microbiota on infection outcome. Cystic fibrosis, chronic obstructive pulmonary disease, COVID-19, and M. tuberculosis studies suggest that surveying the lung microbiota composition can serve as a predictive factor of disease severity and could inform treatment options. In addition to traditional treatment options, probiotics can reverse perturbation-induced repercussions on disease outcomes. The purpose of this review is to speculate on the effects perturbations of the host microbiome can have on coccidioidomycosis progression. To do this, parallels are drawn to aa compilation of other host microbiome infection studies.}, }
@article {pmid37233286, year = {2023}, author = {Liu, D and Smagghe, G and Liu, TX}, title = {Interactions between Entomopathogenic Fungi and Insects and Prospects with Glycans.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {5}, pages = {}, doi = {10.3390/jof9050575}, pmid = {37233286}, issn = {2309-608X}, abstract = {Concerns regarding the ecological and health risks posed by synthetic insecticides have instigated the exploration of alternative methods for controlling insects, such as entomopathogenic fungi (EPF) as biocontrol agents. Therefore, this review discusses their use as a potential alternative to chemical insecticides and especially focuses on the two major ones, Beauveria bassiana and Metarhizium anisopliae, as examples. First, this review exemplifies how B. bassiana- and M. anisopliae-based biopesticides are used in the world. Then, we discuss the mechanism of action by which EPF interacts with insects, focusing on the penetration of the cuticle and the subsequent death of the host. The interactions between EPF and the insect microbiome, as well as the enhancement of the insect immune response, are also summarized. Finally, this review presents recent research that N-glycans may play a role in eliciting an immune response in insects, resulting in the increased expression of immune-related genes and smaller peritrophic matrix pores, reducing insect midgut permeability. Overall, this paper provides an overview of the EPF in insect control and highlights the latest developments relating to the interaction between fungi and insect immunity.}, }
@article {pmid37233280, year = {2023}, author = {Verhasselt, HL and Ramakrishnan, E and Schlag, M and Marchesi, JR and Buer, J and Kleinschnitz, C and Hagenacker, T and Totzeck, A}, title = {Fungal Gut Microbiome in Myasthenia Gravis: A Sub-Analysis of the MYBIOM Study.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {5}, pages = {}, doi = {10.3390/jof9050569}, pmid = {37233280}, issn = {2309-608X}, abstract = {An altered gut microbiota is a possible contributing pathogenic factor in myasthenia gravis (MG), an autoimmune neuromuscular disease. However, the significance of the fungal microbiome is an understudied and neglected part of the intestinal microbiome in MG. We performed a sub-analysis of the MYBIOM study including faecal samples from patients with MG (n = 41), non-inflammatory neurological disorder (NIND, n = 18), chronic inflammatory demyelinating polyradiculoneuropathy (CIDP, n = 6) and healthy volunteers (n = 12) by sequencing the internal transcribed spacer 2 (ITS2). Fungal reads were obtained in 51 out of 77 samples. No differences were found in alpha-diversity indices computed between the MG, NIND, CIDP and HV groups, indicating an unaltered fungal diversity and structure. Overall, four mould species (Penicillium aurantiogriseum, Mycosphaerella tassiana, Cladosporium ramonetellum and Alternaria betae-kenyensis) and five yeast species (Candida. albicans, Candida. sake, Candida. dubliniensis, Pichia deserticola and Kregervanrija delftensis) were identified. Besides one MG patient with abundant Ca. albicans, no prominent dysbiosis in the MG group of the mycobiome was found. Not all fungal sequences within all groups were successfully assigned, so further sub-analysis was withdrawn, limiting robust conclusions.}, }
@article {pmid37232724, year = {2023}, author = {Cañellas-Santos, M and Rosell-Vives, E and Montell, L and Bilbao, A and Goñi-de-Cerio, F and Fernandez-Campos, F}, title = {Anti-Inflammatory and Anti-Quorum Sensing Effect of Camellia sinensis Callus Lysate for Treatment of Acne.}, journal = {Current issues in molecular biology}, volume = {45}, number = {5}, pages = {3997-4016}, doi = {10.3390/cimb45050255}, pmid = {37232724}, issn = {1467-3045}, abstract = {Cutibacterium acnes (C. acnes) is involved in the pathogenesis of acne by inducing inflammation and biofilm formation, along with other virulence factors. A Camellia sinensis (C. sinensis) callus lysate is proposed to reduce these effects. The aim of the present work is to study the anti-inflammatory properties of a callus extract from C. sinensis on C. acnes-stimulated human keratinocytes and the quorum-quenching activities. Keratinocytes were stimulated with thermo-inactivated pathogenic C. acnes and were treated with the herbal lysate (0.25% w/w) to evaluate its anti-inflammatory effect. C. acnes biofilm was developed in vitro and treated with 2.5 and 5% w/w of the lysate to evaluate quorum sensing and the lipase activity. The results showed that the lysate was able to reduce the production of interleukin-6 (IL-6), interleukin-8 (IL-8), tumor necrosis factor-α (TNF-α), and C-X-C motif chemokine ligand 1 (CXCL1), and decrease the nuclear translocation of nuclear factor kappa light chain enhancer of activated B cells (NF-κB). The lysate did not show bactericidal activity but showed diminished biofilm formation, the lipase activity, and the production of autoinducer 2 (AI-2), a member of a family of signaling molecules used in quorum sensing. Therefore, the proposed callus lysate could have the potential to reduce acne-related symptoms without the eradication of C. acnes, which is part of the natural skin microbiome.}, }
@article {pmid37232718, year = {2023}, author = {Fernandes, A and Oliveira, A and Soares, R and Barata, P}, title = {The Effects of Ionizing Radiation on Gut Microbiota: What Can Animal Models Tell Us?-A Systematic Review.}, journal = {Current issues in molecular biology}, volume = {45}, number = {5}, pages = {3877-3910}, doi = {10.3390/cimb45050249}, pmid = {37232718}, issn = {1467-3045}, abstract = {BACKGROUND: The gut microbiota is relatively stable; however, various factors can precipitate an imbalance that is known to be associated with various diseases. We aimed to conduct a systematic literature review of studies reporting the effects of ionizing radiation on the composition, richness, and diversity of the gut microbiota of animals.<br><br>METHODS: A systematic literature search was performed in PubMed, EMBASE, and Cochrane library databases. The standard methodologies expected by Cochrane were utilized.<br><br>RESULTS: We identified 3531 non-duplicated records and selected twenty-nine studies after considering the defined inclusion criteria. The studies were found to be heterogeneous, with significant differences in the chosen populations, methodologies, and outcomes. Overall, we found evidence of an association between ionizing radiation exposure and dysbiosis, with a reduction of microbiota diversity and richness and alterations in the taxonomic composition. Although differences in taxonomic composition varied across studies, Proteobacteria, Verrucomicrobia, Alistipes, and Akkermancia most consistently reported to be relatively more abundant after ionizing radiation exposure, whereas Bacteroidetes, Firmicutes, and Lactobacillus were relatively reduced.<br><br>CONCLUSIONS: This review highlights the effect of ionizing exposure on gut microbiota diversity, richness, and composition. It paves the way for further studies on human subjects regarding gastrointestinal side effects in patients submitted to treatments with ionizing radiation and the development of potential preventive, therapeutic approaches.}, }
@article {pmid37232579, year = {2023}, author = {Levast, B and Fontaine, M and Nancey, S and Dechelotte, P and Doré, J and Lehert, P}, title = {Single-Donor and Pooling Strategies for Fecal Microbiota Transfer Product Preparation in Ulcerative Colitis: A Systematic Review and Meta-analysis.}, journal = {Clinical and translational gastroenterology}, volume = {14}, number = {5}, pages = {e00568}, doi = {10.14309/ctg.0000000000000568}, pmid = {37232579}, issn = {2155-384X}, abstract = {INTRODUCTION: Patients with ulcerative colitis (UC) have a less diverse microbiome than healthy subjects. Multiple studies have evaluated fecal microbiota transfer (FMT) in these patients using different methods of product preparation, doses, and routes of administration. A systematic review and meta-analysis was performed to compare the efficacy of single-donor (SDN) and multidonor (MDN) strategies for product preparation.<br><br>METHODS: Systematic searches were performed in Web of Science, Scopus, PubMed, and Orbit Intelligence for studies comparing FMT products manufactured using SDN or MDN strategies to placebo in patients with UC. Fourteen controlled studies were selected for meta-analysis (10 randomized and 4 nonrandomized). The treatment response was assessed by using fixed- and random-effects models, and the significance of the indirect difference between the interventions was assessed using a network approach.<br><br>RESULTS: Considering all 14 studies, MDN and SDN were superior to placebo in terms of treatment response (risk ratios [RRs]: 4.41 and 1.57, respectively [P &#x2264; 0.001 for both]), and MDN was superior to SDN (RR: 2.81, P = 0.005). Meta-analysis of the 10 studies with high quality of evidence showed that MDN was superior to SDN in terms of treatment response (RR: 2.31, P = 0.042). Results were identical for both models.<br><br>DISCUSSION: There was a significant clinical benefit (remission) for patients with UC who received FMT with products manufactured by MDN strategies. Reduction of donor effect may lead to a gain in microbial diversity that could improve response to treatment. These results may have implications in the treatment approach of other diseases amenable to microbiome manipulation.JOURNAL/cltg/04.03/01720094-202305000-00002/2FFU1/v/2023-05-23T220055Z/r/image-tiff.}, }
@article {pmid37232499, year = {2023}, author = {}, title = {Correction to: Multiomics Analyses Reveal Microbiome-Gut-Brain Crosstalk Centered on Aberrant Gamma-Aminobutyric Acid and Tryptophan Metabolism in Drug-Naïve Patients with First-Episode Schizophrenia.}, journal = {Schizophrenia bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1093/schbul/sbad077}, pmid = {37232499}, issn = {1745-1701}, }
@article {pmid37232427, year = {2023}, author = {Demessant-Flavigny, AL and Connétable, S and Kerob, D and Moreau, M and Aguilar, L and Wollenberg, A}, title = {Skin microbiome dysbiosis and the role of Staphylococcus aureus in atopic dermatitis in adults and children: A narrative review.}, journal = {Journal of the European Academy of Dermatology and Venereology : JEADV}, volume = {37 Suppl 5}, number = {}, pages = {3-17}, doi = {10.1111/jdv.19125}, pmid = {37232427}, issn = {1468-3083}, abstract = {A dysfunctional epidermal barrier, which may be associated with mutations in the filaggrin gene in genetically predisposed individuals or harmful effects of environmental agents and allergens, contributes to the development of atopic dermatitis (AD) due to an interplay between the epithelial barrier, immune defence and the cutaneous microbiome. The skin of patients with AD is frequently over-colonized by biofilm-growing Staphylococcus aureus, especially during flares, causing dysbiosis of the cutaneous microbiota and a decrease in bacterial diversity that inversely correlates with AD severity. Specific changes in the skin microbiome can be present before clinical AD onset in infancy. Additionally, local skin anatomy, lipid content, pH, water activity and sebum secretion differ between children and adults and generally correlate with the predominant microbiota. Considering the importance of S. aureus in AD, treatments aimed at reducing over-colonization to rebalance microbial diversity may help manage AD and reduce flares. Anti-staphylococcal interventions in AD will contribute to a decrease in S. aureus superantigens and proteases that cause damage and inflammation of the skin barrier while concomitantly increasing the proportion of commensal bacteria that secrete antimicrobial molecules that protect healthy skin from invading pathogens. This review summarizes the latest data on targeting skin microbiome dysbiosis and S. aureus over-colonization to treat AD in adults and children. Indirect AD therapies, including emollients 'plus', anti-inflammatory topicals and monoclonal antibodies, may have an impact on S. aureus and help control bacterial diversity. Direct therapies, including antibacterial treatments (antiseptics/topical or systemic antibiotics), and innovative treatments specifically targeting S. aureus (e.g. anti-S. aureus endolysin, and autologous bacteriotherapy), may be effective alternatives to mitigate against an increase in microbial resistance and allow a proportionate increase in the commensal microbiota.}, }
@article {pmid37232281, year = {2023}, author = {El-Heis, S and Crozier, SR and Harvey, NC and Healy, E and Godfrey, KM}, title = {Early life exposure to antibiotics and laxatives in relation to infantile atopic eczema.}, journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology}, volume = {34}, number = {5}, pages = {e13964}, doi = {10.1111/pai.13964}, pmid = {37232281}, issn = {1399-3038}, support = {/ARC_/Arthritis Research UK/United Kingdom ; /BHF_/British Heart Foundation/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; }, }
@article {pmid37232216, year = {2023}, author = {Emerson, KJ and Fontaine, SS and Kohl, KD and Woodley, SK}, title = {Temperature and the microbial environment alter brain morphology in a larval amphibian.}, journal = {The Journal of experimental biology}, volume = {}, number = {}, pages = {}, doi = {10.1242/jeb.245333}, pmid = {37232216}, issn = {1477-9145}, abstract = {Understanding how the global climate impacts the physiology of wildlife animals is of importance. Amphibians are particularly sensitive to climate change, and it is hypothesized that rising temperatures impair their neurodevelopment. Temperature influences the composition of the gut microbiota, which is critical to host neurodevelopment through the microbiota-gut-brain (MGB) axis. Most research investigating the link between the gut microbiota and neurodevelopment occurs in germ-free mammalian model systems, leaving the nature of the MGB axis in non-mammalian wildlife unclear. Here, we tested the hypothesis that the temperature and the microbial environment in which tadpoles were raised shapes neurodevelopment, possibly through the MGB axis. Newly hatched Green Frog tadpoles (Lithobates clamitans) were raised in natural pond water or autoclaved pond water, serving as an experimental manipulation of the microbiota by reducing colonizing microbes, at three different water temperatures: 14°C, 22°C, and 28°C. Neurodevelopment was analyzed through measures of relative brain mass and morphology of brain structures of interest. We found that tadpole development in warmer temperatures increased relative brain mass and optic tectum width and length. Further, tadpole development in autoclaved pond water increased relative optic tectum width and length. Additionally, the interaction of treatments altered relative diencephalon length. Lastly, we found that variation in brain morphology was associated with gut microbial diversity and the relative abundance of individual bacterial taxa. Our results indicate that both environmental temperature and microbial communities influence relative brain mass and shape. Furthermore, we provide some of the first evidence for the MGB axis in amphibians.}, }
@article {pmid37232135, year = {2023}, author = {Chaffer, TJ and Jafarnezhad-Ansariha, F}, title = {The gut-muscle axis shapes exercise performance.}, journal = {The Journal of physiology}, volume = {}, number = {}, pages = {}, doi = {10.1113/JP284905}, pmid = {37232135}, issn = {1469-7793}, }
@article {pmid37231829, year = {2023}, author = {Kawasaki, Y and Kakimoto, K and Tanaka, Y and Shimizu, H and Nishida, K and Numa, K and Kinoshita, N and Tatsumi, Y and Nakazawa, K and Koshiba, R and Hirata, Y and Ota, K and Sakiyama, N and Terazawa, T and Takeuchi, T and Miyazaki, T and Goto, M and Yokota, H and Makizaki, Y and Tanaka, Y and Nakajima, S and Ohno, H and Higuchi, K and Nakamura, S and Nishikawa, H}, title = {Relationship between Chemotherapy-Induced Diarrhea and Intestinal Microbiome Composition.}, journal = {Digestion}, volume = {}, number = {}, pages = {1-13}, doi = {10.1159/000528282}, pmid = {37231829}, issn = {1421-9867}, abstract = {BACKGROUND AND AIM: Fluoropyrimidines (FPs) are key drugs in many chemotherapy regimens; however, recipients are often prone to diarrhea due to gastrointestinal toxicity. Disruption of the intestinal epithelial barrier function by FPs leads to dysbiosis, which may exacerbate intestinal epithelial cell damage as a secondary effect and trigger diarrhea. However, despite studies on chemotherapy-induced changes in the intestinal microbiome of humans, the relationship between dysbiosis and diarrhea is unclear. In this study, we aimed to investigate the relationship between chemotherapy-induced diarrhea and the intestinal microbiome.<br><br>METHODS: We conducted a single-center prospective observational study. Twenty-three patients who received chemotherapy, including FPs as first-line chemotherapy for colorectal cancer, were included. Stool samples were collected before the start of chemotherapy and after one cycle of treatment to analyze intestinal microbiome composition and perform PICRUSt predictive metagenomic analysis.<br><br>RESULTS: Gastrointestinal toxicity was observed in 7 of 23 patients (30.4%), diarrhea was observed in 4 (17.4%), and nausea and anorexia were observed in 3 (13.0%). In 19 patients treated with oral FPs, the &#x3b1; diversity of the microbial community decreased significantly following chemotherapy only in the diarrheal group. At the phylum level, the diarrheal group showed a significant decrease in the abundance of Firmicutes and a significant increase in the abundance of Bacteroidetes with chemotherapy (p = 0.013 and 0.011, respectively). In the same groups, at the genus level, Bifidobacterium abundance was significantly decreased (p = 0.019). In contrast, in the non-diarrheal group, Actinobacteria abundance increased significantly with chemotherapy at the phylum level (p = 0.011). Further, Bifidobacterium, Fusicatenibacter, and Dorea abundance significantly increased at the genus level (p = 0.006, 0.019, and 0.011, respectively). The PICRUSt predictive metagenomic analysis revealed that chemotherapy caused significant differences in membrane transport in KEGG pathway level 2 and in 8 KEGG pathway level 3, including transporters and oxidative phosphorylation in the diarrhea group.<br><br>CONCLUSION: Organic-acid-producing bacteria seem to be involved in diarrhea associated with chemotherapy, including FPs.}, }
@article {pmid37231629, year = {2023}, author = {Li, S and Liao, Y and Jiang, Z and Ji, G}, title = {Life strategies and metabolic interactions of core microbes during thiosulphate-based denitrification.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16430}, pmid = {37231629}, issn = {1462-2920}, abstract = {Sulphur-driven denitrification is a low-cost process for the treatment of nitrate-contaminated water. However, a comprehensive understanding of core populations and microbial interactions of a sulphur-based denitrifying system is lacking. This study presents results from three replicated denitrifying systems amended with thiosulphate and operated under a low C/N ratio. Amplicon sequencing revealed gradual enrichments of a few abundant denitrifiers. Based on genome-centred metagenomics and metatranscriptomics, a core set of microbes was identified in the systems, with Pseudomonas 1 and Thauera 2 being the most abundant ones. Although the replicates showed different enrichments, generalized observations were summarized. Most core populations conserved energy from denitrification coupled with sulphur. Pseudomonas 1 and Thauera 2 were able to finish complete denitrification. Surprisingly, they were also able to synthesize almost all amino acids and vitamins. In contrast, less abundant members, including Pseudomonas 2, were relatively auxotrophic and required an exogenous supply of amino acids and vitamins. The high expression of enzymes involved in biosynthesis and transport systems indicated their syntrophic relationships. The genomic findings suggested life strategies and interactions of the core thiosulphate-based denitrifying microbiome, with implications for nitrate-polluted water remediation.}, }
@article {pmid37231259, year = {2023}, author = {Pinto, Y and Chakraborty, M and Jain, N and Bhatt, AS}, title = {Phage-inclusive profiling of human gut microbiomes with Phanta.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {37231259}, issn = {1546-1696}, abstract = {Due to technical limitations, most gut microbiome studies have focused on prokaryotes, overlooking viruses. Phanta, a virome-inclusive gut microbiome profiling tool, overcomes the limitations of assembly-based viral profiling methods by using customized k-mer-based classification tools and incorporating recently published catalogs of gut viral genomes. Phanta's optimizations consider the small genome size of viruses, sequence homology with prokaryotes and interactions with other gut microbes. Extensive testing of Phanta on simulated data demonstrates that it quickly and accurately quantifies prokaryotes and viruses. When applied to 245 fecal metagenomes from healthy adults, Phanta identifies ~200 viral species per sample, ~5× more than standard assembly-based methods. We observe a ~2:1 ratio between DNA viruses and bacteria, with higher interindividual variability of the gut virome compared to the gut bacteriome. In another cohort, we observe that Phanta performs equally well on bulk versus virus-enriched metagenomes, making it possible to study prokaryotes and viruses in a single experiment, with a single analysis.}, }
@article {pmid37231089, year = {2023}, author = {Kiu, R and Shaw, AG and Sim, K and Acuna-Gonzalez, A and Price, CA and Bedwell, H and Dreger, SA and Fowler, WJ and Cornwell, E and Pickard, D and Belteki, G and Malsom, J and Phillips, S and Young, GR and Schofield, Z and Alcon-Giner, C and Berrington, JE and Stewart, CJ and Dougan, G and Clarke, P and Douce, G and Robinson, SD and Kroll, JS and Hall, LJ}, title = {Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {37231089}, issn = {2058-5276}, abstract = {Clostridium perfringens is an anaerobic toxin-producing bacterium associated with intestinal diseases, particularly in neonatal humans and animals. Infant gut microbiome studies have recently indicated a link between C. perfringens and the preterm infant disease necrotizing enterocolitis (NEC), with specific NEC cases associated with overabundant C. perfringens termed C. perfringens-associated NEC (CPA-NEC). In the present study, we carried out whole-genome sequencing of 272 C. perfringens isolates from 70 infants across 5 hospitals in the United Kingdom. In this retrospective analysis, we performed in-depth genomic analyses (virulence profiling, strain tracking and plasmid analysis) and experimentally characterized pathogenic traits of 31 strains, including 4 from CPA-NEC patients. We found that the gene encoding toxin perfringolysin O, pfoA, was largely deficient in a human-derived hypovirulent lineage, as well as certain colonization factors, in contrast to typical pfoA-encoding virulent lineages. We determined that infant-associated pfoA[+] strains caused significantly more cellular damage than pfoA[-] strains in vitro, and further confirmed this virulence trait in vivo using an oral-challenge C57BL/6 murine model. These findings suggest both the importance of pfoA[+] C. perfringens as a gut pathogen in preterm infants and areas for further investigation, including potential intervention and therapeutic strategies.}, }
@article {pmid37230981, year = {2023}, author = {Feehily, C and O'Neill, IJ and Walsh, CJ and Moore, RL and Killeen, SL and Geraghty, AA and Lawton, EM and Byrne, D and Sanchez-Gallardo, R and Nori, SRC and Nielsen, IB and Wortmann, E and Matthews, E and O'Flaherty, R and Rudd, PM and Groeger, D and Shanahan, F and Saldova, R and McAuliffe, FM and Van Sinderen, D and Cotter, PD}, title = {Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3015}, pmid = {37230981}, issn = {2041-1723}, abstract = {A significant proportion of the infant gut microbiome is considered to be acquired from the mother during and after birth. Thus begins a lifelong and dynamic relationship with microbes that has an enduring impact on host health. Based on a cohort of 135 mother-infant (F = 72, M = 63) dyads (MicrobeMom: ISRCTN53023014), we investigated the phenomenon of microbial strain transfer, with a particular emphasis on the use of a combined metagenomic-culture-based approach to determine the frequency of strain transfer involving members of the genus Bifidobacterium, including species/strains present at low relative abundance. From the isolation and genome sequencing of over 449 bifidobacterial strains, we validate and augment metagenomics-based evidence to reveal strain transfer in almost 50% of dyads. Factors important in strain transfer include vaginal birth, spontaneous rupture of amniotic membranes, and avoidance of intrapartum antibiotics. Importantly, we reveal that several transfer events are uniquely detected employing either cultivation or metagenomic sequencing, highlighting the requirement for a dual approach to obtain an in-depth insight into this transfer process.}, }
@article {pmid37230956, year = {2023}, author = {Song, Y and Cui, YB and Wang, YM and Yu, J and Wang, BL and Wen, QY and Zheng, X}, title = {Donor selection for fecal bacterial transplantation and its combined effects with inulin on early growth and ileal development in chicks.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxad099}, pmid = {37230956}, issn = {1365-2672}, abstract = {AIMS: To select the best donor and investigate its combined effects with inulin on growth performance, and ileal health of chicks.<br><br>METHODS AND RESULTS: The chicks (Hy-line Brown) were treated with fecal microbiota suspension from different breeder hens to select the best donor. Treatment with fecal microbiota transplantation (FMT) alone or in combination with inulin found that it improved gut microbiome in chicks. The organ indexes were increased on 7d, especially the bursa of fabricius index (P&#xa0;<&#xa0;0.05). On 14d, immune performance, ileal morphology, and barrier were improved, simultaneously, the concentration of short-chain fatty acids was also increased. In addition, for the expression of ileal barrier-related genes, Anaerofustis and Clostridium were positively correlated with them (P&#xa0;<&#xa0;0.05), Blautia, Prevotella, Veillonella, and Weissella were the opposite (P&#xa0;<&#xa0;0.05), and RFN20 showed a positive correlation with gut morphology (P&#xa0;<&#xa0;0.05).<br><br>CONCLUSION: Combination of homologous FMT and inulin promoted early growth and intestinal health of chicks.}, }
@article {pmid37230950, year = {2023}, author = {Prüter, H and Gillingham, MAF and Krietsch, J and Kuhn, S and Kempenaers, B}, title = {Sexual transmission may drive pair similarity of the cloacal microbiome in a polyandrous species.}, journal = {The Journal of animal ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1365-2656.13961}, pmid = {37230950}, issn = {1365-2656}, abstract = {All animals host a microbial community within and on their reproductive organs, known as the reproductive microbiome. In free-living birds, studies on the sexual transmission of bacteria have typically focused on a few pathogens instead of the bacterial community as a whole, despite a potential link to reproductive function. Theory predicts higher sexual transmission of the reproductive microbiome in females via the males' ejaculates and higher rates of transmission in promiscuous systems. We studied the cloacal microbiome of breeding individuals of a socially polyandrous, sex-role-reversed shorebird, the red phalarope (Phalaropus fulicarius). We expected (i) higher microbial diversity in females compared to males; (ii) low compositional differentiation between sexes; (iii) lower variation in composition between individuals (i.e. microbiome dispersion) in females than in males; (iv) convergence in composition as the breeding season progresses as a consequence of sexual transmission and/or shared habitat use; and (v) higher similarity in microbial composition between social pair members than between two random opposite-sex individuals. We found no or small between-sex differences in cloacal microbiome diversity/richness and composition. Dispersion of predicted functional pathways was lower in females than in males. As predicted, microbiome dispersion decreased with sampling date relative to clutch initiation of the social pair. Microbiome composition was significantly more similar among social pair members than among two random opposite-sex individuals. Pair membership explained 21.5% of the variation in taxonomic composition and 10.1% of functional profiles, whereas temporal and sex effects explained only 0.6%-1.6%. Consistent with evidence of functional convergence of reproductive microbiomes within pairs, some select taxa and predicted functional pathways were less variable between social pair members than between random opposite-sex individuals. As predicted if sexual transmission of the reproductive microbiome is high, sex differences in microbiome composition were weak in a socially polyandrous system with frequent copulations. Moreover, high within-pair similarity in microbiome composition, particularly for a few taxa spanning the spectrum of the beneficial-pathogenic axis, demonstrates the link between mating behaviour and the reproductive microbiome. Our study is consistent with the hypothesis that sexual transmission plays an important role in driving reproductive microbiome ecology and evolution.}, }
@article {pmid37230685, year = {2022}, author = {Farsijani, S and Cauley, JA and Peddada, SD and Langsetmo, L and Shikany, JM and Orwoll, ES and Ensrud, KE and Cawthon, PM and Newman, AB}, title = {Relation Between Dietary Protein Intake and Gut Microbiome Composition in Community-Dwelling Older Men: Findings from the Osteoporotic Fractures in Men Study (MrOS).}, journal = {The Journal of nutrition}, volume = {152}, number = {12}, pages = {2877-2887}, doi = {10.1093/jn/nxac231}, pmid = {37230685}, issn = {1541-6100}, abstract = {BACKGROUND: Little is known about the association of specific nutrients, especially proteins, on age-related gut dysbiosis.<br><br>OBJECTIVES: To determine the associations between the quantity and sources (vegetable and animal) of dietary protein intake and gut microbiome composition in community-dwelling older men.<br><br>METHODS: We performed a cross-sectional analysis on 775 older men from the Osteoporotic Fractures in Men Study (MrOS) (age 84.2 &#xb1; 4.0 y) with available dietary information and stool samples at visit 4 (2014-2016). Protein intake was estimated from a brief FFQ and adjusted to total energy intake. The gut microbiome composition was determined by 16S (v4) sequencing (processed by DADA2 and SILVA). A total of 11,534 amplicon sequence variants (ASVs) were identified and assigned to 21 phyla with dominance of Firmicutes (45%) and Bacteroidetes (43%). We performed &#x3b1;-diversity, &#x3b2;-diversity, and taxa abundance (by Analysis of Compositions of Microbiomes with Bias Correction [ANCOM-BC]) to determine the associations between protein intake and the gut microbiome.<br><br>RESULTS: Median protein intake was 0.7 g/(kg body weight &#xb7; d). Participants with higher energy-adjusted protein intakes had higher Shannon and Chao1 &#x3b1;-diversity indices (P < 0.05). For &#x3b2;-diversity analysis, participants with higher protein intakes had a different center in weighted and unweighted UniFrac Principal Co-ordinates Analysis (PCoA) compared with those with lower intake (P < 0.05), adjusted for age, race, education, clinical center, batch number, fiber and energy intake, weight, height, and medications. Similarly, higher protein consumptions from either animal or vegetable sources were associated with higher gut microbiome diversity. Several genus-level ASVs, including Christensenellaceae, Veillonella, Haemophilus, and Klebsiella were more abundant in participants with higher protein intakes, whereas Clostridiales bacterium DTU089 and Desulfovibrio were more abundant in participants with lower protein intake (Bonferroni corrected P < 0.05).<br><br>CONCLUSIONS: We observed significant associations between protein intake and gut microbiome diversity in community-living older men. Further studies are needed to elucidate the mediation role of the gut microbiome on the relation between protein intake and health outcomes in older adults.}, }
@article {pmid37230671, year = {2022}, author = {Hendrixson, DT and Naskidashvili, N and Stephenson, KB and Laury, ML and Koroma, AS and Manary, MJ}, title = {An Alternative Oat-Containing, Ready-To-Use, Therapeutic Food Does Not Alter Intestinal Permeability or the 16S Ribosomal RNA Fecal Microbiome Configuration Among Children With Severe Malnutrition in Sierra Leone: A Randomized Controlled Trial.}, journal = {The Journal of nutrition}, volume = {152}, number = {12}, pages = {2744-2753}, doi = {10.1093/jn/nxac207}, pmid = {37230671}, issn = {1541-6100}, abstract = {BACKGROUND: Previously, a novel oat ready-to-use therapeutic food (o-RUTF) resulted in improved recovery from severe acute malnutrition (SAM) when compared to a standard RUTF (s-RUTF). The o-RUTF contained 18% oat, while the s-RUTF has no cereal ingredients.<br><br>OBJECTIVES: We determined the effects of o-RUTF on intestinal permeability, as measured by lactulose permeability, and the 16S ribosomal RNA (rRNA) fecal microbiome configuration of children with SAM.<br><br>METHODS: This was a prospective, randomized, double-blinded, controlled clinical trial. Sierra Leonean children aged 6-59 mo with SAM, defined by a midupper arm circumference < 11.5 cm, were randomized to receive o-RUTF or s-RUTF. All children received 7 d of amoxicillin per guidelines. Lactulose permeability testing and fecal 16S rRNA sequencing were performed at baseline and after 4 wk of therapy. The change in lactulose permeability was the primary outcome, while the fecal 16S rRNA configuration at 4 wk was a secondary outcome.<br><br>RESULTS: Of the 129 children enrolled, lactulose permeability testing was completed by 100 at baseline and 82 at week 4. After 4 wk of therapeutic feeding, there were no differences in lactulose permeability between the o-RUTF and s-RUTF groups (P = 0.84), and over half of children had increased lactulose permeability (50% s-RUTF compared with 58% o-RUTF, mean difference = -7.5%; 95% CI: -29.2, 15.2; P = 0.50). After 4 wk of feeding, there were no differences in the 16S rRNA configurations between the o-RUTF and s-RUTF groups (Permanova, 999 permutations; P = 0.648; pseudo-F = 0.581), nor were there differences in &#x3b1; or &#x3b2; diversity.<br><br>CONCLUSIONS: Despite remarkably different compositions of o-RUTF and s-RUTF, no differences were identified in lactulose permeability or the fecal 16S rRNA configuration among children with SAM receiving these foods. These results suggest that the o-RUTF exerts its beneficial effects through mechanisms other than reducing intestinal permeability or altering the fecal 16S configuration. This trial was registered at clinicaltrials.gov as NCT04334538.}, }
@article {pmid37230357, year = {2023}, author = {Jiang, Y and Huang, S and Zhu, F and Guo, X and Zhang, X and Zhu, M and Zhang, Y and Xue, S}, title = {Long-term weathering difference in soil-like indicators of bauxite residue mediates the multifunctionality driven by microbial communities.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164377}, doi = {10.1016/j.scitotenv.2023.164377}, pmid = {37230357}, issn = {1879-1026}, abstract = {Long-term weathering enhances the stability of ecosystem services and alters the microbiome, however, its influences on the relationship between microbial diversity and multifunctionality are still poorly understood. Hereby, 156 samples (0-20 cm) from five artificially divided functional zones including central bauxite residue zone (BR), the zone near residential area (RA), the zone near dry farming area (DR), the zone near natural forest area (NF), and the zone near grassland and forest area (GF) were collected in a typical disposal area to determine the heterogeneity and development of biotic and abiotic properties of bauxite residue. Residues in BR and RA exhibited higher values of pH, EC, heavy metals, and exchangeable sodium percentage compared to those in NF and GF. Our results showed a positive correlation between multifunctionality and soil-like quality during long-term weathering. Microbial diversity and microbial network complexity responded positively to multifunctionality within the microbial community, which was parallel with ecosystem functioning. Long-term weathering promoted oligotrophs-dominated bacterial assemblages (mostly Acidobacteria and Chloroflexi) and suppressed copiotrophs (including Proteobacteria and Bacteroidota), while the response of fungal communities was lower. Rare taxa from bacterial oligotrophs were particularly important at the current stage for maintaining ecosystem services and ensuring microbial network complexity. Our results underscore the significance of microbial ecophysiological strategies in response to changes in multifunctionality during long-term weathering, and highlight the necessity of conserving and augmenting the abundance of rare taxa to ensure the stable provision of ecosystem functions in bauxite residue disposal areas.}, }
@article {pmid37230354, year = {2023}, author = {Mandal, M and Das, S and Roy, A and Rakwal, R and Jones, OAH and Popek, R and Agrawal, GK and Sarkar, A}, title = {Interactive relations between plants, phyllosphere microbial community, and particulate matter pollution.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164352}, doi = {10.1016/j.scitotenv.2023.164352}, pmid = {37230354}, issn = {1879-1026}, abstract = {Particulate matter (PM) pollution poses a significant risk to many ecosystems; as sessile organisms, plants are at particular risk from PM pollution since they cannot move away from it. Microorganisms are essential components of ecosystems that can help macro-organisms to cope with pollutants (such as PM). In the phyllosphere (the aerial/above-ground parts of plants colonized by microbial communities), plant-microbe associations have been found to promote plant development while also increasing host resilience to biotic and abiotic stressors. This review discusses how plant-microbe symbiosis in the phyllosphere potentially affects host survivability and efficiency in the face of pollution and factors such as climate change. Evidence is presented that plant-microbe associations can be beneficial, such as by degrading pollutants, yet also bring disadvantages, such as causing the loss of symbiotic organisms and/or inducing disease. It is suggested that plant genetics is a fundamental driver of the phyllosphere microbiome assembly, connecting phyllosphere microbiota to plant health management in adverse conditions. Finally, potential ways that essential community ecological processes might influence plant-microbe partnerships in the face of Anthropocene-linked changes and what this might mean for environmental management are discussed.}, }
@article {pmid37229965, year = {2023}, author = {Nadal-Molero, F and Campos-Lopez, A and Tur-Moya, J and Martin-Cuadrado, AB}, title = {Microbial community on industrial salty bovine hides: From the slaughterhouse to the salting.}, journal = {Systematic and applied microbiology}, volume = {46}, number = {4}, pages = {126421}, doi = {10.1016/j.syapm.2023.126421}, pmid = {37229965}, issn = {1618-0984}, abstract = {The leather-making industry is an age-old industry and desiccation with salt has been one of the most used methodologies for obtaining valuable skins. However, halophiles may proliferate and affect the integrity of the hide-collagen structure, as well as leading to undesirable red colorations or less-frequent purple stains. To understand the basis of these industrial hide contaminations, the microbial community from raw hide samples, salt-cured samples and four different industrial salts, was analyzed by 16S rRNA gene metabarcoding together with standard cultivation methods. Comparison of raw hides and correctly cured hides revealed a core microbiome that was absent from contaminated hides. In addition, archaea were missing from well-cured hides, whereas Psychrobacter and Acinetobacter were highly represented (23 % and 17.4 %, respectively). In damaged hides, only a few operational taxonomic units (OTUs), from among the hundreds detected, were able to proliferate and, remarkably, a single Halomonas OTU represented 57.66 % of the reads. Halobacteria, mainly Halovenus, Halorubrum and Halovivax, increased by up to 36.24-39.5 % in the red- and purple-affected hides. The major contaminants were isolated and hide infections, together with collagenase activity, were evaluated. The results showed that hides enriched with the non-pigmented isolate Halomonas utahensis COIN160 damaged the collagen fibers similarly to Halorubrum, and together they were considered to be one of the major causes. Putative degrading inhibitors were also identified from among the Alkalibacillus isolates. It was concluded that hide contaminations were driven by clonal outbreaks of a few specific microbes, which may have been non-pigmented collagen degraders. Acinetobacter and Alkalibacillus, members of the core microbiome of raw and well-cured salted hides, are suggested as hide contaminant inhibitors that need further analysis.}, }
@article {pmid37229916, year = {2023}, author = {Mir, HD and Giorgini, G and Di Marzo, V}, title = {The emerging role of the endocannabinoidome-gut microbiome axis in eating disorders.}, journal = {Psychoneuroendocrinology}, volume = {154}, number = {}, pages = {106295}, doi = {10.1016/j.psyneuen.2023.106295}, pmid = {37229916}, issn = {1873-3360}, abstract = {Among the sources of chemical signals regulating food intake, energy metabolism and body weight, few have attracted recently as much attention as the expanded endocannabinoid system, or endocannabinoidome (eCBome), and the gut microbiome, the two systems on which this review article is focussed. Therefore, it is legitimate to expect that these two systems also play a major role in the etiopathology of eating disorders (EDs), in particular of anorexia nervosa, bulimia nervosa and binge-eating disorder. The major mechanisms through which, also via interactions with other endogenous signaling systems, the eCBome, with its several lipid mediators and receptors, and the gut microbiome, via its variety of microbial kingdoms, phyla and species, and armamentarium of metabolites, intervene in these disorders, are described here, based on several published studies in either experimental models or patients. Additionally, in view of the emerging multi-faceted cross-talk mechanisms between these two complex systems, we discuss the possibility that the eCBome-gut microbiome axis is also involved in EDs.}, }
@article {pmid37229712, year = {2023}, author = {Roughgarden, J}, title = {Holobiont Evolution: Population Theory for the Hologenome.}, journal = {The American naturalist}, volume = {201}, number = {6}, pages = {763-778}, doi = {10.1086/723782}, pmid = {37229712}, issn = {1537-5323}, abstract = {AbstractThis article develops mathematical theory for the population dynamics of microbiomes with their hosts and for holobiont evolution caused by holobiont selection. The objective is to account for the formation of microbiome-host integration. Microbial population dynamic parameters must mesh with the host's for coexistence. A horizontally transmitted microbiome is a genetic system with "collective inheritance." The microbial source pool in the environment corresponds to the gamete pool for nuclear genes. Poisson sampling of the microbial source pool corresponds to binomial sampling of the gamete pool. However, holobiont selection on the microbiome does not lead to a counterpart of the Hardy-Weinberg law or to directional selection that always fixes microbial genes conferring the highest holobiont fitness. A microbe might strike an optimal fitness balance between lowering its within-host fitness while increasing holobiont fitness. Such microbes are replaced by otherwise identical microbes that contribute nothing to holobiont fitness. This replacement can be reversed by hosts that initiate immune responses to nonhelpful microbes. This discrimination leads to microbial species sorting. Host-orchestrated species sorting followed by microbial competition, rather than coevolution or multilevel selection, is predicted to be the cause of microbiome-host integration.}, }
@article {pmid37229125, year = {2023}, author = {Costa, JM and Egipto, R and Aguiar, FC and Marques, P and Nogales, A and Madeira, M}, title = {The role of soil temperature in mediterranean vineyards in a climate change context.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1145137}, doi = {10.3389/fpls.2023.1145137}, pmid = {37229125}, issn = {1664-462X}, abstract = {The wine sector faces important challenges related to sustainability issues and the impact of climate change. More frequent extreme climate conditions (high temperatures coupled with severe drought periods) have become a matter of concern for the wine sector of typically dry and warm regions, such as the Mediterranean European countries. Soil is a natural resource crucial to sustaining the equilibrium of ecosystems, economic growth and people's prosperity worldwide. In viticulture, soils have a great influence on crop performance (growth, yield and berry composition) and wine quality, as the soil is a central component of the terroir. Soil temperature (ST) affects multiple physical, chemical and biological processes occurring in the soil as well as in plants growing on it. Moreover, the impact of ST is stronger in row crops such as grapevine, since it favors soil exposition to radiation and favors evapotranspiration. The role of ST on crop performance remains poorly described, especially under more extreme climatic conditions. Therefore, a better understanding of the impact of ST in vineyards (vine plants, weeds, microbiota) can help to better manage and predict vineyards' performance, plant-soil relations and soil microbiome under more extreme climate conditions. In addition, soil and plant thermal data can be integrated into Decision Support Systems (DSS) to support vineyard management. In this paper, the role of ST in Mediterranean vineyards is reviewed namely in terms of its effect on vines' ecophysiological and agronomical performance and its relation with soil properties and soil management strategies. The potential use of imaging approaches, e.g. thermography, is discussed as an alternative or complementary tool to assess ST and vertical canopy temperature profiles/gradients in vineyards. Soil management strategies to mitigate the negative impact of climate change, optimize ST variation and crop thermal microclimate (leaf and berry) are proposed and discussed, with emphasis on Mediterranean systems.}, }
@article {pmid37228982, year = {2023}, author = {Mohan, A and Godugu, S and Joshi, SS and Shah, KB and Vanka, SC and Shakil, H and P, D and Veliginti, S and Sure, PS and Goranti, J}, title = {Gut-brain axis: altered microbiome and depression - review.}, journal = {Annals of medicine and surgery (2012)}, volume = {85}, number = {5}, pages = {1784-1789}, doi = {10.1097/MS9.0000000000000573}, pmid = {37228982}, issn = {2049-0801}, abstract = {The concept of a 'gut-brain axis' was recently developed when the complex communications between the brain and the gut became evident. The interaction may affect emotions, motivation, mood, and higher cognitive functions as well as gut homeostasis. Human microbe symbiosis's merits are now acknowledged to transcend human mental health. Research has recently indicated that the gut-brain axis plays a vital role in brain health maintenance. The term 'gut-brain axis' can only partially capture the intricacy of these interactions. Dysbiosis of the gut commensals has been seen in patients with psychiatric diseases, such as depression. Major depressive disorder is caused by complicated interactions between the individual gene and the environment. In a forced swimming test, P. Zheng et al. discovered that germ-free mice with no gut microbiota had a shorter immobility duration than healthy mice. More radical effects were expressed on the use of probiotics rather than prebiotics and postbiotics in reducing the symptoms of depression in patients with major depressive disorder. One of prime importance can be given to exploring more microbiota to investigate the better therapeutic effects of probiotics, prebiotics, and postbiotics.}, }
@article {pmid37228957, year = {2023}, author = {Mhanna, A and Alshehabi, Z}, title = {The microbiota-gut-brain axis and three common neurological disorders: a mini-review.}, journal = {Annals of medicine and surgery (2012)}, volume = {85}, number = {5}, pages = {1780-1783}, doi = {10.1097/MS9.0000000000000552}, pmid = {37228957}, issn = {2049-0801}, abstract = {Neurological disorders are an important cause of disability and death globally. Recently, a large body of research shows that the gut microbiome affects the brain and its conditions, through the gut-brain axis. The purpose of this mini-review is to provide a brief overview of the relationship between the microbiota-gut-brain axis in three neurological disorders: epilepsy, Parkinson's disease, and migraine. The authors chose these three disorders because of their burdensome and great effect on health care. We live on a microbial planet. Before humans, microorganisms existed for a hundred million years. Today, there are trillions of these microbes living in our bodies, it is called human microbiota. These organisms have a crucial role in our homeostasis and survival. Most of the human microbiota live in the gut. The number of gut microbiota is much more than the number of body cells. Gut microbiota has been regarded as a crucial regulator of the gut-brain axis. The discovery of the microbiota-gut-brain axis is described as a major advancement in neuroscience because it influences the pathophysiology of several neurological and psychiatric disorders. From this, more studies of the microbiota-gut-brain axis are needed in the future, to provide a better understanding of brain disorders and so that better treatment and prognosis.}, }
@article {pmid37228436, year = {2023}, author = {Shaikh, N and Kurs-Lasky, M and Liu, H and Rajakumar, V and Qureini, H and Conway, IO and Lee, MC and Lee, S}, title = {Biomarkers for febrile urinary tract infection in children.}, journal = {Frontiers in pediatrics}, volume = {11}, number = {}, pages = {1163546}, doi = {10.3389/fped.2023.1163546}, pmid = {37228436}, issn = {2296-2360}, abstract = {BACKGROUND: The current reference standard for pediatric urinary tract infection (UTI) screening, the leukocyte esterase (LE) dipstick test, has suboptimal accuracy. The objective of this study was to compare the accuracy of novel urinary biomarkers to that of the LE test.<br><br>METHODS: We prospectively enrolled febrile children who were evaluated for UTI based on their presenting symptoms. We compared the accuracy of urinary biomarkers to that of the test.<br><br>RESULTS: We included 374 children (50 with UTI, 324 without UTI, ages 1-35 months) and examined 35 urinary biomarkers. The urinary biomarkers that best discriminated between febrile children with and without UTI were urinary neutrophil gelatinase-associated lipocalin (NGAL), IL-1&#x3b2;, CXCL1, and IL-8. Of all examined urinary biomarkers, the urinary NGAL had the highest accuracy with a sensitivity of 90% (CI: 82-98) and a specificity of 96% (CI: 93-98).<br><br>CONCLUSION: Because the sensitivity of the urinary NGAL test is slightly higher than that of the LE test, it can potentially reduce missed UTI cases. Limitations of using urinary NGAL over LE include increased cost and complexity. Further investigation is warranted to determine the cost-effectiveness of urinary NGAL as a screening test for UTI.}, }
@article {pmid37228418, year = {2023}, author = {Babalola, OO and Akanmu, AO and Fadiji, AE}, title = {Dataset of shotgun metagenomic evaluation of lettuce (Lactuta sativa L.) rhizosphere microbiome.}, journal = {Data in brief}, volume = {48}, number = {}, pages = {109214}, doi = {10.1016/j.dib.2023.109214}, pmid = {37228418}, issn = {2352-3409}, abstract = {Lettuce (Lactuca sativa L.) is an important vegetable grown and consumed across the world, including South Africa and its rhizosphere constitutes a dynamic community of root associated microbes. Dataset of the microbial community profile of the lettuce rhizospheric soils obtained from Talton, Gauteng Province of South Africa was subjected to metagenomic evaluation using the shotgun approach. The whole DNA isolated from the community was sequenced using NovaSeq 6000 system (Illumina). The raw data obtained consists of 129,063,513.33 sequences with an average length of 200 base pairs and 60.6% Guanine + Cytosine content. The metagenome data has been deposited to the National Centre for Biotechnology Information SRA under the bioproject number PRJNA763048. The downstream analysis alongside taxonomical annotation carried out using an online server MG-RAST, showed the community analysis as being made up of archaea (0.95%), eukaryotes (1.36%), viruses (0.04%), while 97.65% of the sequences were classified as bacteria. A sum of 25 bacteria, 20 eukaryotic and 4 archaea phyla were identified. The predominant genera were Acinetobacter (4.85%), Pseudomonas (3.41%), Streptomyces (2.79%), Candidatus solibacter (1.93%), Burkholderia (1.65%), Bradyrhizobium (1.51%) and Mycobacterium (1.31%). Annotation using Cluster of Orthologous Group (COG) showed 23.91% of the sequenced data were for metabolic function, 33.08% for chemical process and signaling while 6.42% were poorly characterized. Furthermore, the subsystem annotation method showed that sequences were majorly associated with carbohydrates (12.86%), clustering-based subsystems (12.68%), and genes coding for amino acids and derivatives (10.04%), all of which could serve in growth promotion and plant management.}, }
@article {pmid37228387, year = {2023}, author = {Fung, DLX and Li, X and Leung, CK and Hu, P}, title = {A self-knowledge distillation-driven CNN-LSTM model for predicting disease outcomes using longitudinal microbiome data.}, journal = {Bioinformatics advances}, volume = {3}, number = {1}, pages = {vbad059}, doi = {10.1093/bioadv/vbad059}, pmid = {37228387}, issn = {2635-0041}, abstract = {MOTIVATION: Human microbiome is complex and highly dynamic in nature. Dynamic patterns of the microbiome can capture more information than single point inference as it contains the temporal changes information. However, dynamic information of the human microbiome can be hard to be captured due to the complexity of obtaining the longitudinal data with a large volume of missing data that in conjunction with heterogeneity may provide a challenge for the data analysis.<br><br>RESULTS: We propose using an efficient hybrid deep learning architecture convolutional neural network-long short-term memory, which combines with self-knowledge distillation to create highly accurate models to analyze the longitudinal microbiome profiles to predict disease outcomes. Using our proposed models, we analyzed the datasets from Predicting Response to Standardized Pediatric Colitis Therapy (PROTECT) study and DIABIMMUNE study. We showed the significant improvement in the area under the receiver operating characteristic curve scores, achieving 0.889 and 0.798 on PROTECT study and DIABIMMUNE study, respectively, compared with state-of-the-art temporal deep learning models. Our findings provide an effective artificial intelligence-based tool to predict disease outcomes using longitudinal microbiome profiles from collected patients.<br><br>The data and source code can be accessed at https://github.com/darylfung96/UC-disease-TL.}, }
@article {pmid37228376, year = {2023}, author = {Piloto-Sardiñas, E and Cano-Argüelles, AL and Maitre, A and Wu-Chuang, A and Mateos-Hernández, L and Corduneanu, A and Obregón, D and Oleaga, A and Pérez-Sánchez, R and Cabezas-Cruz, A}, title = {Comparison of salivary gland and midgut microbiome in the soft ticks Ornithodoros erraticus and Ornithodoros moubata.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1173609}, doi = {10.3389/fmicb.2023.1173609}, pmid = {37228376}, issn = {1664-302X}, abstract = {INTRODUCTION: Ornithodoros erraticus and Ornithodoros moubata are the main vectors of African swine fever virus (ASFV) and the human relapsing fever spirochetes Borrelia hispanica and Borrelia crocidurae in the Mediterranean region and Borrelia duttoni in continental Africa. Manipulation of the tick microbiome has been shown to reduce vector fitness and competence in tick vectors, suggesting that the identification of key microbial players associated with tick tissues can inform interventions such as anti-microbiota vaccines to block pathogen development in the midgut and/or salivary glands.<br><br>METHODS: In this study, we analyzed and compared the microbiome of the salivary glands and midgut of O. erraticus and O. moubata. For the taxonomic and functional characterization of the tissue-specific microbiome, we used 16S rRNA amplicon sequencing and prediction of metabolic profiles using PICRUSt2. Co-occurrence networks were built to characterize the community assembly and identify keystone taxa in each tick species.<br><br>RESULTS: Our results revealed differences in the composition, diversity, and assembly of the bacterial microbiome of salivary glands and midgut within each tick species, but differences were more noticeable in O. moubata. Differences were also found in the microbiome of each tissue, salivary gland and midgut, between species. However, the 'Core Association Networks (CAN)' analysis revealed conserved patterns of interacting taxa in tissues within and between tick species. Different keystone taxa were identified in O. erraticus and O. moubata tissues, but Muribaculaceae and Alistipes were found as keystone taxa in the salivary glands of both tick species which justifies their use as anti-microbiota vaccine candidates to alter the microbiome and reduce tick fitness and/or block pathogen transmission. The high similarity of predicted metabolic pathways profiles between tissues of the two tick species suggests that taxonomic variability of the microbiome is not associated with significant changes in microbial functional profiles.<br><br>CONCLUSION: We conclude that the taxonomic structure of the microbiome in O. erraticus and O. moubata is tissue-specific, suggesting niche partitioning of bacterial communities associated to these soft ticks. However, shared keystone taxa and conserved patterns of interacting taxa between tissues and tick species suggest the presence of key microbial players that could be used as anti-microbiota vaccine candidates to affect tick physiology and/or pathogen colonization.}, }
@article {pmid37228370, year = {2023}, author = {Thijssen, M and Tacke, F and Van Espen, L and Cassiman, D and Naser Aldine, M and Nevens, F and Van Ranst, M and Matthijnssens, J and Pourkarim, MR}, title = {Plasma virome dynamics in chronic hepatitis B virus infected patients.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1172574}, doi = {10.3389/fmicb.2023.1172574}, pmid = {37228370}, issn = {1664-302X}, abstract = {The virome remains an understudied domain of the human microbiome. The role of commensal viruses on the outcome of infections with known pathogens is not well characterized. In this study we aimed to characterize the longitudinal plasma virome dynamics in chronic hepatitis B virus (HBV) infected patients. Eighty-five longitudinal plasma samples were collected from 12 chronic HBV infected individuals that were classified in the four stages of HBV infection. The virome was characterized with an optimized viral extraction protocol and deep-sequenced on a NextSeq 2500 platform. The plasma virome was primarily composed of members of the Anello- Flavi-, and Hepadnaviridae (HBV) families. The virome structure and dynamics did not correlate with the different stages of chronic HBV infection nor with the administration of antiviral therapy. We observed a higher intrapersonal similarity of viral contigs. Genomic analysis of viruses observed in multiple timepoint demonstrated the presence of a dynamic community. This study comprehensively assessed the blood virome structure in chronic HBV infected individuals and provided insights in the longitudinal development of this viral community.}, }
@article {pmid37228141, year = {2023}, author = {Young, BD and Rosales, SM and Enochs, IC and Kolodziej, G and Formel, N and Moura, A and D'Alonso, GL and Traylor-Knowles, N}, title = {Different disease inoculations cause common responses of the host immune system and prokaryotic component of the microbiome in Acropora palmata.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0286293}, doi = {10.1371/journal.pone.0286293}, pmid = {37228141}, issn = {1932-6203}, abstract = {Reef-building corals contain a complex consortium of organisms, a holobiont, which responds dynamically to disease, making pathogen identification difficult. While coral transcriptomics and microbiome communities have previously been characterized, similarities and differences in their responses to different pathogenic sources has not yet been assessed. In this study, we inoculated four genets of the Caribbean branching coral Acropora palmata with a known coral pathogen (Serratia marcescens) and white band disease. We then characterized the coral's transcriptomic and prokaryotic microbiomes' (prokaryiome) responses to the disease inoculations, as well as how these responses were affected by a short-term heat stress prior to disease inoculation. We found strong commonality in both the transcriptomic and prokaryiomes responses, regardless of disease inoculation. Differences, however, were observed between inoculated corals that either remained healthy or developed active disease signs. Transcriptomic co-expression analysis identified that corals inoculated with disease increased gene expression of immune, wound healing, and fatty acid metabolic processes. Co-abundance analysis of the prokaryiome identified sets of both healthy-and-disease-state bacteria, while co-expression analysis of the prokaryiomes' inferred metagenomic function revealed infected corals' prokaryiomes shifted from free-living to biofilm states, as well as increasing metabolic processes. The short-term heat stress did not increase disease susceptibility for any of the four genets with any of the disease inoculations, and there was only a weak effect captured in the coral hosts' transcriptomic and prokaryiomes response. Genet identity, however, was a major driver of the transcriptomic variance, primarily due to differences in baseline immune gene expression. Despite genotypic differences in baseline gene expression, we have identified a common response for components of the coral holobiont to different disease inoculations. This work has identified genes and prokaryiome members that can be focused on for future coral disease work, specifically, putative disease diagnostic tools.}, }
@article {pmid37228117, year = {2023}, author = {Puri, SR and Almeida, E and Elangovan, S and Labossiere, A and Collins, C and Ramsey, M and Kim, J}, title = {Mechanistic Assessment of Metabolic Interaction between Single Oral Commensal Cells by Scanning Electrochemical Microscopy.}, journal = {Analytical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.analchem.3c01498}, pmid = {37228117}, issn = {1520-6882}, abstract = {The human oral microbiome heavily influences the status of oral and systemic diseases through different microbial compositions and complex signaling between microbes. Recent evidence suggests that investigation of interactions between oral microbes can be utilized to understand how stable communities are maintained and how they may preserve health. Herein, we investigate two highly abundant species in the human supragingival plaque, Streptococcus mitis and Corynebacterium matruchotii, to elucidate their real-time chemical communication in commensal harmony. Specifically, we apply nanoscale scanning electrochemical microscopy (SECM) using a submicropipet-supported interface between two immiscible electrolyte solutions as an SECM probe not only to image the permeability of S. mitis and C. matruchotii membranes to tetraethylammonium (TEA[+]) probe ions but also to real-time visualize the metabolic interaction between two microbes via lactate production/consumption at a single-cell level. The metabolic relationship between two strains is quantitatively assessed by determining (1) the passive permeability of both bacterial membranes of 2.4 × 10[-4] cm/s to the free diffusion of TEA[+], (2) 0.5 mM of the lactate concentration produced by a single S. mitis strain at a rate of 2.7 × 10[-4] cm/s, and (3) a lactate oxidation rate ≥5.0 × 10[6] s[-1] by an individual C. matruchotii strain. Significantly, this study, for the first time, describes a mechanism of in situ metabolic interaction between oral commensals at the single-cell level through quantitative analysis, which supports the observed in vivo spatial arrangements of these microbes.}, }
@article {pmid37227689, year = {2023}, author = {Vega-Sagardía, M and Cabezón, EC and Delgado, J and Ruiz-Moyano, S and Garrido, D}, title = {Screening Microbial Interactions During Inulin Utilization Reveals Strong Competition and Proteomic Changes in Lacticaseibacillus paracasei M38.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {37227689}, issn = {1867-1314}, abstract = {Competition for resources is a common microbial interaction in the gut microbiome. Inulin is a well-studied prebiotic dietary fiber that profoundly shapes gut microbiome composition. Several community members and some probiotics, such as Lacticaseibacillus paracasei, deploy multiple molecular strategies to access fructans. In this work, we screened bacterial interactions during inulin utilization in representative gut microbes. Unidirectional and bidirectional assays were used to evaluate the effects of microbial interactions and global proteomic changes on inulin utilization. Unidirectional assays showed the total or partial consumption of inulin by many gut microbes. Partial consumption was associated with cross-feeding of fructose or short oligosaccharides. However, bidirectional assays showed strong competition from L. paracasei M38 against other gut microbes, reducing the growth and quantity of proteins found in the latter. L. paracasei dominated and outcompeted other inulin utilizers, such as Ligilactobacillus ruminis PT16, Bifidobacterium longum PT4, and Bacteroides fragilis HM714. The importance of strain-specific characteristics of L. paracasei, such as its high fitness for inulin consumption, allows it to be favored for bacterial competence. Proteomic studies indicated an increase in inulin-degrading enzymes in co-cultures, such as β-fructosidase, 6-phosphofructokinase, the PTS D-fructose system, and ABC transporters. These results reveal that intestinal metabolic interactions are strain-dependent and might result in cross-feeding or competition depending on total or partial consumption of inulin. Partial degradation of inulin by certain bacteria favors coexistence. However, when L. paracasei M38 totally degrades the fiber, this does not happen. The synergy of this prebiotic with L. paracasei M38 could determine the predominance in the host as a potential probiotic.}, }
@article {pmid37227280, year = {2023}, author = {Cai, F and Zhou, C and Jiao, N and Liang, X and Ye, Z and Chen, W and Yang, Q and Peng, H and Tang, Y and Niu, C and Zhao, G and Wang, Z and Zhang, G and Yu, X}, title = {Systematic Microbiome Dysbiosis Is Associated with IgA Nephropathy.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0520222}, doi = {10.1128/spectrum.05202-22}, pmid = {37227280}, issn = {2165-0497}, abstract = {IgA nephropathy (IgAN) is reportedly associated with microbial dysbiosis. However, the microbiome dysregulation of IgAN patients across multiple niches remains unclear. To gain a systematic understanding of microbial dysbiosis, we conducted large-scale 16S rRNA gene sequencing in IgAN patients and healthy volunteers across 1,732 oral, pharynx, gut, and urine samples. We observed a niche-specific increase of several opportunistic pathogens, including Bergeyella and Capnocytophaga in the oral and pharynx, whereas some beneficial commensals decreased in IgAN patients. Similar alterations were also observed in the early versus advanced stage of chronic kidney disease (CKD) progression. Moreover, Bergeyella, Capnocytophaga, and Comamonas in the oral and pharynx were positively associated with creatinine and urea, indicating renal lesions. Random forest classifiers were developed by using the microbial abundance to predict IgAN, achieving an optimal accuracy of 0.879 in the discovery phase and 0.780 in the validation phase. IMPORTANCE This study provides microbial profiles of IgAN across multiple niches and underlines the potential of these biomarkers as promising, noninvasive tools with which to differentiate IgAN patients for clinical applications.}, }
@article {pmid37227087, year = {2023}, author = {Rahman, AT and Shin, J and Whang, CH and Jung, W and Yoo, D and Seo, C and Cho, BK and Jon, S}, title = {Bilirubin Nanomedicine Rescues Intestinal Barrier Destruction and Restores Mucosal Immunity in Colitis.}, journal = {ACS nano}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsnano.3c03252}, pmid = {37227087}, issn = {1936-086X}, abstract = {Inflammatory bowel disease (IBD) manifests as intestinal barrier destruction, mucosal immunity dysregulation, and disrupted gut microbiome homeostasis. Conventional anti-inflammatory medications for IBD therapy partially alleviate symptoms but are unable to restore normal barrier and immune function. Here, we report a nanomedicine comprising bilirubin (BR)-attached low-molecular-weight, water-soluble chitosan nanoparticles (LMWC-BRNPs), that promotes restoration of the intestinal barrier, mucosal immunity, and the gut microbiome, thereby exerting robust therapeutic efficacy. In a mouse model of dextran sulfate sodium salt (DSS)-induced colitis, orally administered LMWC-BRNPs were retained in the GI tract much longer than other nonmucoadhesive BRNPs owing to the mucoadhesiveness of LMWC via electrostatic interaction. Treatment with LMWC-BRNPs led to considerable recovery of the damaged intestinal barrier compared with the current IBD medication, 5-aminosalicylic acid (5-ASA). Orally administered LMWC-BRNPs were taken up by pro-inflammatory macrophages and inhibited their activity. They also concurrently increased the population of regulatory T cells, thereby leading to the recovery of dysregulated mucosal immunity. An analysis of the gut microbiome revealed that LMWC-BRNPs treatment significantly attenuated the increase Turicibacter, an inflammation-related microorganism, resulting in protection of gut microbiome homeostasis. Taken together, our findings indicate that LMWC-BRNPs restored normal functions of the intestine and have high potential for use as a nanomedicine for IBD therapy.}, }
@article {pmid37226793, year = {2023}, author = {Jamialahmadi, T and Simental-Mendia, LE and Zengin, G and Almahmeed, W and Kesharwani, P and Sahebkar, A}, title = {Meta-analysis of the impact of bariatric surgery on circulating TMAO levels as a predictor of cardiovascular disease risk.}, journal = {Current medicinal chemistry}, volume = {}, number = {}, pages = {}, doi = {10.2174/0929867330666230523155750}, pmid = {37226793}, issn = {1875-533X}, abstract = {INTRODUCTION: Trimethylamine N-oxide (TMAO) is a metabolite of the gut microbiota that is considered a cardiovascular risk factor. Because bariatric surgery (BS) produces changes in the composition of the gut microbiota, the production of TMAO can be compromised. Thus, the purpose of this meta-analysis was to determine the effect of BS on circulating TMAO levels.<br><br>METHODS: A systematic search was carried on in Embase, PubMed, Web of Science, and Scopus databases. The meta-analysis was conducted using Comprehensive Meta-Analysis (CMA) V2 software. The overall effect size was determined by a random-effects meta-analysis and the leave-one-out approach.<br><br>RESULTS: Random-effects meta-analysis of 5 studies consisting of 142 subjects demonstrated a significant increase in circulating TMAO levels after BS (SMD: 1.190, 95% CI: 0.521, 1.858, p<0.001; I2:89.30%).<br><br>CONCLUSION: Considering that levels of TMAO are affected after BS due to gut microbial metabolism alteration, there has been a significant elevation in TMAO concentrations observed to occur after BS in obese subjects.}, }
@article {pmid37226644, year = {2023}, author = {Brescia, F and Sillo, F and Franchi, E and Pietrini, I and Montesano, V and Marino, G and Haworth, M and Zampieri, E and Fusini, D and Schillaci, M and Papa, R and Santamarina, C and Vita, F and Chitarra, W and Nerva, L and Petruzzelli, G and Mennone, C and Centritto, M and Balestrini, R}, title = {The 'microbiome counterattack': Insights on the soil and root-associated microbiome in diverse chickpea and lentil genotypes after an erratic rainfall event.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.13167}, pmid = {37226644}, issn = {1758-2229}, abstract = {Legumes maintain soil fertility thanks to their associated microbiota but are threatened by climate change that causes soil microbial community structural and functional modifications. The core microbiome associated with different chickpea and lentil genotypes was described after an unexpected climatic event. Results showed that chickpea and lentil bulk soil microbiomes varied significantly between two sampling time points, the first immediately after the rainfall and the second 2 weeks later. Rhizobia were associated with the soil of the more productive chickpea genotypes in terms of flower and fruit number. The root-associated bacteria and fungi were surveyed in lentil genotypes, considering that several parcels showed disease symptoms. The metabarcoding analysis revealed that reads related to fungal pathogens were significantly associated with one lentil genotype. A lentil core prokaryotic community common to all genotypes was identified as well as a genotype-specific one. A higher number of specific bacterial taxa and an enhanced tolerance to fungal diseases characterized a lentil landrace compared to the commercial varieties. This outcome supported the hypothesis that locally adapted landraces might have a high recruiting efficiency of beneficial soil microbes.}, }
@article {pmid37226596, year = {2023}, author = {Medina, JM and Queller, DC and Strassmann, JE and Garcia, JR}, title = {The social amoeba dictyostelium discoideum rescues paraburkholderia hayleyella, but not P. agricolaris, from interspecific competition.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiad055}, pmid = {37226596}, issn = {1574-6941}, abstract = {Bacterial endosymbionts can provide benefits for their eukaryotic hosts, but it is often unclear if endosymbionts benefit from these relationships. The social amoeba Dictyostelium discoideum associates with three species of Paraburkholderia endosymbionts, including P. agricolaris and P. hayleyella. These endosymbionts can be costly to host but are beneficial in certain contexts because they allow D. discoideum to carry prey bacteria through the dispersal stage. In experiments where no other species are present, P. hayleyella benefits from D. discoideum while P. agricolaris does not. However, the presence of other species may influence this symbiosis. We tested if P. agricolaris and P. hayleyella benefit from D. discoideum in the context of resource competition with Klebsiella pneumoniae, the typical laboratory prey of D. discoideum. Without D. discoideum, K. pneumoniae depressed the growth of both Paraburkholderia symbionts, consistent with competition. P. hayleyella was more harmed by interspecific competition than P. agricolaris. We found that P. hayleyella was rescued from competition by D. discoideum while P. agricolaris was not. This may be because P. hayleyella is more specialized as an endosymbiont; it has a highly reduced genome compared to P. agricolaris and may have lost genes relevant for resource competition outside of its host.}, }
@article {pmid37226420, year = {2023}, author = {Schimmel, P and Stahl, B and Knol, J and Belzer, C}, title = {The infant gut microbiota: in pursuit of non-protein nitrogen.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2211917}, doi = {10.1080/19490976.2023.2211917}, pmid = {37226420}, issn = {1949-0984}, abstract = {Diet shapes our gut microbiome from the day we are born. The contribution of dietary non-protein nitrogen to normal and healthy nitrogen cycling in the infant gut is scarcely described. Herein, we review in vitro and in vivo findings that show the impact of Human Milk Nitrogen (HMN) on the gut microbiota that colonizes the gut in early human life. We describe that several non-protein nitrogen sources, that include creatine, creatinine, urea, polyamines and free amino acids, are key in establishing the bifidobacterium-dominated microbiome and thus are bifidogenic. Furthermore, several parts of HMN-related metabolism are associated with a healthy infant gut and commensal microbiota. We illustrate an overlap and great diversity in accessibility of HMN by large parts of the infant gut microbiota. This review nonetheless shows the importance of research on HMN and its effects on the activity and composition of the infant gut microbiota and its potential effect on early life infant health.}, }
@article {pmid37226227, year = {2023}, author = {Maksoud, R and Magawa, C and Eaton-Fitch, N and Thapaliya, K and Marshall-Gradisnik, S}, title = {Biomarkers for myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS): a systematic review.}, journal = {BMC medicine}, volume = {21}, number = {1}, pages = {189}, pmid = {37226227}, issn = {1741-7015}, abstract = {BACKGROUND: Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a multifaceted condition that affects most body systems. There is currently no known diagnostic biomarker; instead, diagnosis is dependent on application of symptom-based case criteria following exclusion of any other potential medical conditions. While there are some studies that report potential biomarkers for ME/CFS, their efficacy has not been validated. The aim of this systematic review is to collate and appraise literature pertaining to a potential biomarker(s) which may effectively differentiate ME/CFS patients from healthy controls.<br><br>METHODS: This systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses and Cochrane review guidelines. PubMed, Embase and Scopus were systematically searched for articles containing "biomarker" and "ME/CFS" keywords in the abstract or title and if they included the following criteria: (1) were observational studies published between December 1994 and April 2022; (2) involved adult human participants; (3) full text is available in English (4) original research; (5) diagnosis of ME/CFS patients made according to the Fukuda criteria (1994), Canadian Consensus Criteria (2003), International Consensus Criteria (2011) or Institute of Medicine Criteria (2015); (6) study investigated potential biomarkers of ME/CFS compared to healthy controls. Quality and Bias were assessed using the Joanna Briggs Institute Critical Appraisal Checklist for Case Control Studies.<br><br>RESULTS: A total of 101 publications were included in this systematic review. Potential biomarkers ranged from genetic/epigenetic (19.8%), immunological (29.7%), metabolomics/mitochondrial/microbiome (14.85%), endovascular/circulatory (17.82%), neurological (7.92%), ion channel (8.91%) and physical dysfunction biomarkers (8.91%). Most of the potential biomarkers reported were blood-based (79.2%). Use of lymphocytes as a model to investigate ME/CFS pathology was prominent among immune-based biomarkers. Most biomarkers had secondary (43.56%) or tertiary (54.47%) selectivity, which is the ability for the biomarker to identify a disease-causing agent, and a moderate (59.40%) to complex (39.60%) ease-of-detection, including the requirement of specialised equipment.<br><br>CONCLUSIONS: All potential ME/CFS biomarkers differed in efficiency, quality, and translatability as a diagnostic marker. Reproducibility of findings between the included publications were limited, however, several studies validated the involvement of immune dysfunction in the pathology of ME/CFS and the use of lymphocytes as a model to investigate the pathomechanism of illness. The heterogeneity shown across many of the included studies highlights the need for multidisciplinary research and uniform protocols in ME/CFS biomarker research.}, }
@article {pmid37226179, year = {2023}, author = {Dunlap, DG and Yang, L and Qin, S and Li, K and Fitch, A and Huang, L and McVerry, BJ and Hand, TW and Methé, BA and Morris, A}, title = {Magnetic-activated cell sorting identifies a unique lung microbiome community.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {117}, pmid = {37226179}, issn = {2049-2618}, abstract = {BACKGROUND: The advent of culture-independent, next-generation DNA sequencing has led to the discovery of distinct lung bacterial communities. Studies of lung microbiome taxonomy often reveal only subtle differences between health and disease, but host recognition and response may distinguish the members of similar bacterial communities in different populations. Magnetic-activated cell sorting has been applied to the gut microbiome to identify the numbers and types of bacteria eliciting a humoral response. We adapted this technique to examine the populations of immunoglobulin-bound bacteria in the lung.<br><br>METHODS: Sixty-four individuals underwent bronchoalveolar lavage (BAL). We separated immunoglobulin G-bound bacteria using magnetic-activated cell sorting and sequenced the 16S rRNA gene on the Illumina MiSeq platform. We compared microbial sequencing data in IgG-bound bacterial communities compared to raw BAL then examined the differences in individuals with and without HIV as a representative disease state.<br><br>RESULTS: Immunoglobulin G-bound bacteria were identified in all individuals. The community structure differed when compared to raw BAL, and there was a greater abundance of Pseudomonas and fewer oral bacteria in IgG-bound BAL. Examination of IgG-bound communities in individuals with HIV demonstrated the differences in Ig-bound bacteria by HIV status that were not seen in a comparison of raw BAL, and greater numbers of immunoglobulin-bound bacteria were associated with higher pulmonary cytokine levels.<br><br>CONCLUSIONS: We report a novel application of magnetic-activated cell sorting to identify immunoglobulin G-bound bacteria in the lung. This technique identified distinct bacterial communities which differed in composition from raw bronchoalveolar lavage, revealing the differences not detected by traditional analyses. Cytokine response was also associated with differential immunoglobulin binding of lung bacteria, suggesting the functional importance of these communities. Video Abstract.}, }
@article {pmid37226109, year = {2023}, author = {Truong, AT and Kang, JE and Yoo, MS and Nguyen, TT and Youn, SY and Yoon, SS and Cho, YS}, title = {Probiotic candidates for controlling Paenibacillus larvae, a causative agent of American foulbrood disease in honey bee.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {150}, pmid = {37226109}, issn = {1471-2180}, abstract = {BACKGROUND: American foulbrood (AFB) disease caused by Paenibacillus larvae is dangerous, and threatens beekeeping. The eco-friendly treatment method using probiotics is expected to be the prospective method for controlling this pathogen in honey bees. Therefore, this study investigated the bacterial species that have antimicrobial activity against P. larvae.<br><br>RESULTS: Overall, 67 strains of the gut microbiome were isolated and identified in three phyla; the isolates had the following prevalence rates: Firmicutes 41/67 (61.19%), Actinobacteria 24/67 (35.82%), and Proteobacteria 2/67 (2.99%). Antimicrobial properties against P. larvae on agar plates were seen in 20 isolates of the genus Lactobacillus, Firmicutes phylum. Six representative strains from each species (L. apis HSY8_B25, L. panisapium PKH2_L3, L. melliventris HSY3_B5, L. kimbladii AHS3_B36, L. kullabergensis OMG2_B25, and L. mellis OMG2_B33) with the largest inhibition zones on agar plates were selected for in vitro larvae rearing challenges. The results showed that three isolates (L. apis HSY8_B25, L. panisapium PKH2_L3, and L. melliventris HSY3_B5) had the potential to be probiotic candidates with the properties of safety to larvae, inhibition against P. larvae in infected larvae, and high adhesion ability.<br><br>CONCLUSIONS: Overall, 20 strains of the genus Lactobacillus with antimicrobial properties against P. larvae were identified in this study. Three representative strains from different species (L. apis HSY8_B25, L. panisapium PKH2_L3, and L. melliventris HSY3_B5) were evaluated to be potential probiotic candidates and were selected for probiotic development for the prevention of AFB. Importantly, the species L. panisapium isolated from larvae was identified with antimicrobial activity for the first time in this study.}, }
@article {pmid37225918, year = {2023}, author = {Elston, KM and Phillips, LE and Leonard, SP and Young, E and Holley, JC and Ahsanullah, T and McReynolds, B and Moran, NA and Barrick, JE}, title = {The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {49}, pmid = {37225918}, issn = {2730-6151}, abstract = {Toolkits of plasmids and genetic parts streamline the process of assembling DNA constructs and engineering microbes. Many of these kits were designed with specific industrial or laboratory microbes in mind. For researchers interested in non-model microbial systems, it is often unclear which tools and techniques will function in newly isolated strains. To address this challenge, we designed the Pathfinder toolkit for quickly determining the compatibility of a bacterium with different plasmid components. Pathfinder plasmids combine three different broad-host-range origins of replication with multiple antibiotic resistance cassettes and reporters, so that sets of parts can be rapidly screened through multiplex conjugation. We first tested these plasmids in Escherichia coli, a strain of Sodalis praecaptivus that colonizes insects, and a Rosenbergiella isolate from leafhoppers. Then, we used the Pathfinder plasmids to engineer previously unstudied bacteria from the family Orbaceae that were isolated from several fly species. Engineered Orbaceae strains were able to colonize Drosophila melanogaster and could be visualized in fly guts. Orbaceae are common and abundant in the guts of wild-caught flies but have not been included in laboratory studies of how the Drosophila microbiome affects fly health. Thus, this work provides foundational genetic tools for studying microbial ecology and host-associated microbes, including bacteria that are a key constituent of the gut microbiome of a model insect species.}, }
@article {pmid37225687, year = {2023}, author = {Zhao, F and Yang, L and Zhang, T and Zhuang, D and Wu, Q and Yu, J and Tian, C and Zhang, Z}, title = {Gut microbiome signatures of extreme environment adaption in Tibetan pig.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {27}, pmid = {37225687}, issn = {2055-5008}, abstract = {Tibetan pigs (TPs) can adapt to the extreme environments in the Tibetan plateau implicated by their self-genome signals, but little is known about roles of the gut microbiota in the host adaption. Here, we reconstructed 8210 metagenome-assembled genomes from TPs (n = 65) living in high-altitude and low-altitude captive pigs (87 from China-CPs and 200 from Europe-EPs) that were clustered into 1050 species-level genome bins (SGBs) at the threshold of 95% average nucleotide identity. 73.47% of SGBs represented new species. The gut microbial community structure analysis based on 1,048 SGBs showed that TPs was significantly different from low-altitude captive pigs. TP-associated SGBs enabled to digest multiple complex polysaccharides, including cellulose, hemicellulose, chitin and pectin. Especially, we found TPs showed the most common enrichment of phyla Fibrobacterota and Elusimicrobia, which were involved in the productions of short- and medium-chain fatty acids (acetic acid, butanoate and propanoate; octanomic, decanoic and dodecanoic acids), as well as in the biosynthesis of lactate, 20 essential amino acids, multiple B vitamins (B1, B2, B3, B5, B7 and B9) and cofactors. Unexpectedly, Fibrobacterota solely showed powerful metabolic capacity, including the synthesis of acetic acid, alanine, histidine, arginine, tryptophan, serine, threonine, valine, B2, B5, B9, heme and tetrahydrofolate. These metabolites might contribute to host adaptation to high-altitude, such as energy harvesting and resistance against hypoxia and ultraviolet radiation. This study provides insights into understanding the role of gut microbiome played in mammalian high-altitude adaptation and discovers some potential microbes as probiotics for improving animal health.}, }
@article {pmid37225588, year = {2023}, author = {Khurana, R and Brand, T and Tapio, I and Bayat, AR}, title = {Effect of a garlic and citrus extract supplement on performance, rumen fermentation, methane production, and rumen microbiome of dairy cows.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2022-22838}, pmid = {37225588}, issn = {1525-3198}, abstract = {The aim of this trial was to determine the effect of a garlic and citrus extract supplement (GCE) on the performance, rumen fermentation, methane emissions, and rumen microbiome of dairy cows. Fourteen multiparous Nordic Red cows in mid-lactation from the research herd of Luke (Jokioinen, Finland) were allocated to 7 blocks in a complete randomized block design based on body weight, days in milk, dry matter intake (DMI), and milk yield. Animals within each block were randomly allocated to a diet with or without GCE. The experimental period for each block of cows (one for each of the control and GCE groups) consisted of 14 d of adaptation followed by 4 d of methane measurements inside the open circuit respiration chambers, with the first day being considered as acclimatization. Data were analyzed using the GLM procedure of SAS (SAS Institute Inc.). Methane production (g/d) and methane intensity (g/kg of energy-corrected milk) were lower by 10.3 and 11.7%, respectively, and methane yield (g/kg of DMI) tended to be lower by 9.7% in cows fed GCE compared with the control. Dry matter intake, milk production, and milk composition were similar between treatments. Rumen pH and total volatile fatty acid concentrations in rumen fluid were similar, whereas GCE tended to increase molar propionate concentration and decrease the molar ratio of acetate to propionate. Supplementation with GCE resulted in greater abundance of Succinivibrionaceae, which was associated with reduced methane. The relative abundance of the strict anaerobic Methanobrevibacter genus was reduced by GCE. The change in microbial community and rumen propionate proportion may explain the decrease in enteric methane emissions. In conclusion, feeding GCE to dairy cows for 18 d modified rumen fermentation and microbiota, leading to reduced methane production and intensity without compromising DMI or milk production in dairy cows. This could be an effective strategy for enteric methane mitigation of dairy cows.}, }
@article {pmid37225326, year = {2023}, author = {Ahrodia, T and Kandiyal, B and Das, B}, title = {Microbiota and epigenetics: Health impact.}, journal = {Progress in molecular biology and translational science}, volume = {198}, number = {}, pages = {93-117}, doi = {10.1016/bs.pmbts.2023.03.018}, pmid = {37225326}, issn = {1878-0814}, abstract = {Epigenetic changes associated with disease development and progressions are of increasing importance because of their potential diagnostic and therapeutic applications. Several epigenetic changes associated with chronic metabolic disorders have been studied in various diseases. Epigenetic changes are mostly modulated by environmental factors, including the human microbiota living in different parts of our bodies. The microbial structural components and the microbially derived metabolites directly interact with host cells, thereby maintaining homeostasis. Microbiome dysbiosis, on the other hand, is known to produce elevated levels of disease-linked metabolites, which may directly affect a host metabolic pathway or induce epigenetic changes that can lead to disease development. Despite their important role in host physiology and signal transduction, there has been little research into the mechanics and pathways associated with epigenetic modifications. This chapter focuses on the relationship between microbes and their epigenetic effects in diseased pathology, as well as on the regulation and metabolism of the dietary options available to the microbes. Furthermore, this chapter also provides a prospective link between these two important phenomena, termed "Microbiome and Epigenetics."}, }
@article {pmid37224780, year = {2023}, author = {Wang, CQ and Su, Z and Dai, CG and Song, JL and Qian, B}, title = {Multi-omics analysis reveals BDE47 induces depression-like behaviors in mice by interfering with the 2-arachidonoyl glycerol-associated microbiota-gut-brain axis.}, journal = {Ecotoxicology and environmental safety}, volume = {259}, number = {}, pages = {115041}, doi = {10.1016/j.ecoenv.2023.115041}, pmid = {37224780}, issn = {1090-2414}, abstract = {2,2',4,4'-tetrabromodiphenyl ether (BDE47) is a foodborne environmental risk factor for depression, but the pathogenic mechanism has yet to be fully characterized. In this study, we clarified the effect of BDE47 on depression in mice. The abnormal regulation of the microbiome-gut-brain axis is evidenced closely associated with the development of depression. Using RNA sequencing, metabolomics, and 16s rDNA amplicon sequencing, the role of the microbiome-gut-brain axis in depression was also explored. The results showed that BDE47 exposure increased depression-like behaviors in mice but inhibited the learning memory ability of mice. The RNA sequencing analysis showed that BDE47 exposure disrupted dopamine transmission in the brain of mice. Meanwhile, BDE47 exposure reduced protein levels of tyrosine hydroxylase (TH) and dopamine transporter (DAT), activated astrocytes and microglia cells, and increased protein levels of NLRP3, IL-6, IL-1β, and TNF-α in the brain of mice. The 16 s rDNA sequencing analysis showed that BDE47 exposure disrupted microbiota communities in the intestinal contents of mice, and faecalibaculum was the most increased genus. Moreover, BDE47 exposure increased the levels of IL-6, IL-1β, and TNF-α in the colon and serum of mice but decreased the levels of tight junction protein ZO-1 and Occludin in the colon and brain of mice. In addition, the metabolomic analysis revealed that BDE47 exposure induced metabolic disorders of arachidonic acid and neurotransmitter 2-Arachidonoyl glycerol (2-AG) was one of the most decreased metabolites. Correlation analysis further revealed gut microbial dysbiosis, particularly faecalibaculum, is associated with altered gut metabolites and serum cytokines in response to BDE47 exposure. Our results suggest that BDE47 might induce depression-like behavior in mice through gut microbial dysbiosis. The mechanism might be associated with the inhibited 2-AG signaling and increased inflammatory signaling in the gut-brain axis.}, }
@article {pmid37224779, year = {2023}, author = {Zhang, X and Jia, X and Wang, S and Xin, J and Sun, N and Wang, Y and Zhang, X and Wan, Z and Fan, J and Li, H and Bai, Y and Ni, X and Huang, Y and Wang, H and Ma, H}, title = {Disrupted gut microbiota aggravates spatial memory dysfunction induced by high altitude exposure: A link between plateau environment and microbiome-gut-brain axis.}, journal = {Ecotoxicology and environmental safety}, volume = {259}, number = {}, pages = {115035}, doi = {10.1016/j.ecoenv.2023.115035}, pmid = {37224779}, issn = {1090-2414}, abstract = {Approximately 400 million people work and live in high-altitude areas and suffer from memory dysfunction worldwide. Until now, the role of the intestinal flora in plateau-induced brain damage has rarely been reported. To address this, we investigated the effect of intestinal flora on spatial memory impairment induced by high altitudes based on the microbiome-gut-brain axis theory. C57BL/6 mice were divided into three groups: control, high-altitude (HA), and high-altitude antibiotic treatment (HAA) group. The HA and HAA groups were exposed to a low-pressure oxygen chamber that simulated an altitude of 4000 m above sea level (m. a. s.l.) for 14 days, with the air pressure in the chamber set at 60-65 kPa. The results showed that spatial memory dysfunction induced by the high-altitude environment was aggravated by antibiotic treatment, manifesting as lowered escape latency and hippocampal memory-related proteins (BDNF and PSD-95). 16 S rRNA sequencing showed a remarkable separation of the ileal microbiota among the three groups. Antibiotic treatment exacerbated the reduced richness and diversity of the ileal microbiota in mice in the HA group. Lactobacillaceae were the main target bacteria and were significantly reduced in the HA group, which was exacerbated by antibiotic treatment. Meanwhile, reduced intestinal permeability and ileal immune function in mice exposed high-altitude environment was also aggravated by antibiotic treatment, as indicated by the lowered tight junction proteins and IL-1β and IFN-γ levels. Furthermore, indicator species analysis and Netshift co-analysis revealed that Lactobacillaceae (ASV11) and Corynebacteriaceae (ASV78, ASV25, and ASV47) play important roles in high-altitude exposure-induced memory dysfunction. Interestingly, ASV78 was negatively correlated with IL-1β and IFN-γ levels, indicating that ASV78 may be induced by reduced ileal immune function, which mediates high-altitude environment exposure-induced memory dysfunction. This study provides evidence that the intestinal flora is effective in preventing brain dysfunction caused by exposure to high-altitude environments, suggesting a relationship between the microbiome-gut-brain axis and altitude exposure.}, }
@article {pmid37224760, year = {2023}, author = {Dixon, R and Egan, S and Hughes, S and Chapman, B}, title = {The Sexome - A proof of concept study into microbial transfer between heterosexual couples after sexual intercourse.}, journal = {Forensic science international}, volume = {348}, number = {}, pages = {111711}, doi = {10.1016/j.forsciint.2023.111711}, pmid = {37224760}, issn = {1872-6283}, abstract = {The detection and recovery of male DNA post-assault is important in sexual assault investigations, particularly where an offender is unknown to the victim. The collection of DNA evidence often occurs when the female victim undergoes a forensic medical assessment. Analysis regularly results in mixed autosomal DNA profiles with both victim and perpetrator DNA, often making it difficult to interpret a male profile suitable for DNA database searching. While short tandem repeat (STR) profiling of the male Y-chromosome is often used to overcome this challenge, successful identification of an individual can be hindered by the paternal inheritance pattern of Y-STRs and small Y-STR databases. Human microbiome research has suggested that a person's microbial diversity is unique. Therefore microbiome analysis using Massively Parallel Sequencing (MPS) could serve as a useful adjunct method of perpetrator identification. This study aimed to identify bacteria taxa that were unique to each participant and compare the bacterial communities found on their genitals both pre- and post-coitus. Samples were collected from six male-female sexual partner pairs. Volunteers were asked to self-collect low vaginal (females) and penis shaft and glans (males) samples before and after intercourse. Samples were extracted using the PureLink™ Microbiome DNA Purification Kit. Extracted DNA underwent library preparation using primers targeting the V3-V4 hypervariable regions of the bacterial 16S rRNA gene (∼450 bp). Libraries were sequenced on the Illumina MiSeq® platform. From the sequence data derived, statistical analysis was performed to investigate if bacteria sequences could be used to infer contact between each male-female pairing. Unique bacterial signatures were detected in low frequencies (<1%) in male and female participants pre-coitus. The data indicated a significant disruption to microbial diversity post-coitus in all samples. A transfer of the female microbiome during intercourse was most significant. As expected, one couple who did not use a barrier contraceptive yielded the most microbial transfer and disruption to diversity demonstrating a proof-of-concept in the utility of microbiome interrogation for sexual assault cases. Further genomic analysis is needed to confirm species and subspecies classification of bacteria that may produce a unique microbial profile that could then be used to identify a specific individual.}, }
@article {pmid37224677, year = {2023}, author = {Keshava, C and Nicolai, S and Vulimiri, SV and Cruz, FA and Ghoreishi, N and Knueppel, S and Lenzner, A and Tarnow, P and Vanselow, JT and Schulz, B and Persad, A and Baker, N and Thayer, KA and Williams, AJ and Pirow, R}, title = {Application of systematic evidence mapping to identify available data on the potential human health hazards of selected market-relevant azo dyes.}, journal = {Environment international}, volume = {176}, number = {}, pages = {107952}, doi = {10.1016/j.envint.2023.107952}, pmid = {37224677}, issn = {1873-6750}, abstract = {BACKGROUND: Azo dyes are used in textiles and leather clothing. Human exposure can occur from wearing textiles containing azo dyes. Since the body's enzymes and microbiome can cleave azo dyes, potentially resulting in mutagenic or carcinogenic metabolites, there is also an indirect health concern on the parent compounds. While several hazardous azo dyes are banned, many more are still in use that have not been evaluated systematically for potential health concerns. This systematic evidence map (SEM) aims to compile and categorize the available toxicological evidence on the potential human health risks of a set of 30 market-relevant azo dyes.<br><br>METHODS: Peer-reviewed and gray literature was searched and over 20,000 studies were identified. These were filtered using Sciome Workbench for Interactive computer-Facilitated Text-mining (SWIFT) Review software with evidence stream tags (human, animal, in vitro) yielding 12,800 unique records. SWIFT Active (a machine-learning software) further facilitated title/abstract screening. DistillerSR software was used for additional title/abstract, full-text screening, and data extraction.<br><br>RESULTS: 187 studies were identified that met populations, exposures, comparators, and outcomes (PECO) criteria. From this pool, 54 human, 78 animal, and 61 genotoxicity studies were extracted into a literature inventory. Toxicological evidence was abundant for three azo dyes (also used as food additives) and sparse for five of the remaining 27 compounds. Complementary search in ECHA's REACH database for summaries of unpublished study reports revealed evidence for all 30 dyes. The question arose of how this information can be fed into an SEM process. Proper identification of prioritized dyes from various databases (including U.S. EPA's CompTox Chemicals Dashboard) turned out to be a challenge. Evidence compiled by this SEM project can be evaluated for subsequent use in problem formulation efforts to inform potential regulatory needs and prepare for a more efficient and targeted evaluation in the future for human health assessments.}, }
@article {pmid37224614, year = {2023}, author = {Le Graverand, Q and Marie-Etancelin, C and Meynadier, A and Weisbecker, JL and Marcon, D and Tortereau, F}, title = {Predicting feed efficiency traits in growing lambs from their ruminal microbiota.}, journal = {Animal : an international journal of animal bioscience}, volume = {17}, number = {6}, pages = {100824}, doi = {10.1016/j.animal.2023.100824}, pmid = {37224614}, issn = {1751-732X}, abstract = {Selecting feed-efficient sheep could improve the sustainability of this livestock production. However, most sheep breeding companies cannot afford to record feed intake to select feed-efficient animals. Past studies underlined the potential of omics data, including microbiota metabarcoding data, as proxies for feed efficiency. The study involved 277 Romane lambs from two lines divergently selected for residual feed intake (RFI). There were two objectives: check the consequences of selecting for feed efficiency over the rumen microbiota, and assess the predictive ability of the rumen microbiota for host traits. The study assessed two contrasting diets (concentrate diet and mixed diet) and two microbial groups (prokaryotes and eukaryotes). Discriminant analyses did not highlight any significant effect of sheep selection for residual feed intake on the rumen microbiota composition. Indeed, prokaryotic and eukaryotic microbiota compositions poorly discriminated the RFI lines, with averaged balanced error rates ranging from 45% to 55%. Correlations between host traits (feed efficiency and production traits) and their predictions from microbiota data varied between -0.07 and 0.56, depending on the trait, diet and sequencing. Feed intake was the most accurately predicted trait. However, predictions from fixed effects and BW were more accurate than or as accurate as predictions from the microbiota. Environmental effects can greatly affect the variability of microbiota compositions. Considering batch and environmental effects should be paramount when the predictive ability of the microbiota is assessed. This study argues why metabarcoding the rumen microbiota is not the best way to predict meat sheep production traits: fixed effects and BW were more cost-effective proxies and they led to similar or better predictive accuracies than microbiota metabarcoding (16S and 18S sequencing).}, }
@article {pmid37224578, year = {2023}, author = {Saeed, A and Yasmin, A and Baig, M and Ahmed, MA and Farooqi, ZU}, title = {Streptococcus lactarius MB622 and Streptococcus salivarius MB620 isolated from human milk reduce chemokine IL-8 production in response to TNF-α in Caco-2 cell line, an exploratory study.}, journal = {Cytokine}, volume = {168}, number = {}, pages = {156232}, doi = {10.1016/j.cyto.2023.156232}, pmid = {37224578}, issn = {1096-0023}, abstract = {Streptococci are a predominant genera of the human milk microbiome. Among different lactic acid bacteria (LAB) a few Streptococcal strains are also considered as probiotics. Probiotic bacteria are reported to modulate immunity when consumed in adequate amount and bacterial hydrophobicity can be considered as a preliminary experiment for the adhesive capability of probiotic bacteria to the epithelial cells. The present study aimed to investigate the probiotic, hydrophobic and immune modulation property of Streptococcus lactarius MB622 and Streptococcus salivarius MB620, isolated from human milk. S. lactarius MB622 and S. salivarius MB620 displayed higher hydrophobicity (78 % and 59 % respectively) in addition to intrinsic probiotic properties such as gram positive classification, catalase negative activity, resistance to artificially stimulated gastric juice and gastrointestinal bile salt concentration. In conclusion Streptococcus lactarius MB622 and Streptococcus salivarius MB620 isolated from human milk when administered in sufficient amount and for certain duration could be used to reduce inflammation inside the colon by reducing the production of inflammatory booster (IL-8) in diseased state.}, }
@article {pmid37224470, year = {2023}, author = {Hall Reynolds, F and Tusa, MG and Banks, SL}, title = {Toe Web Infections, the Microbiome, and Toe Web Psoriasis: A Review.}, journal = {Advances in skin &amp; wound care}, volume = {}, number = {}, pages = {}, doi = {10.1097/01.ASW.0000933728.56221.82}, pmid = {37224470}, issn = {1538-8654}, abstract = {OBJECTIVE: To present the toe web space as an anatomically, physiologically, and pathologically unique part of the human body; characterize toe web infections and discuss why they occur; and highlight toe web psoriasis as an uncommon condition that providers should consider if toe web intertrigo does not respond to treatment.<br><br>DATA SOURCE: This review encompassed many years of clinical observation and photographs, medical textbooks, and a literature search of MEDLINE, PubMed, and Google Scholar.<br><br>STUDY SELECTION: Primary research keywords included intertrigo, toe web intertrigo, toe web infection, tinea pedis, microbiome, skin microbiome, toe web microbiome, ecology, psoriasis, psoriasis microbiome, intertriginous psoriasis, and Wood's lamp. More than 190 journal articles met the search criteria.<br><br>DATA EXTRACTION: The authors sought data relating to what makes for a healthy toe web space and what makes for disease. They extracted and collated relevant information to compare and contrast between sources.<br><br>DATA SYNTHESIS: After understanding the normal toe web space and the microorganisms that normally reside there, the authors investigated why infections occur, how they should be treated, what complications may result, and what other diseases occur in the toe web area.<br><br>CONCLUSIONS: This review of toe web infection illustrates the effect of the microbiome and reports a rare form of psoriasis that is usually misdiagnosed as athlete's foot. The toe web space is a unique part of the human body that can be affected by a variety of both common and unusual conditions.}, }
@article {pmid37224399, year = {2023}, author = {}, title = {A Scoping Review of Neonatal Opioid Withdrawal and the Infant Gut Microbiome: Does Human Milk Optimize Infant Outcomes?.}, journal = {Advances in neonatal care : official journal of the National Association of Neonatal Nurses}, volume = {23}, number = {3}, pages = {E59}, doi = {10.1097/ANC.0000000000001084}, pmid = {37224399}, issn = {1536-0911}, }
@article {pmid37224176, year = {2023}, author = {Cobb, J and Soliman, SSM and Retuerto, M and Quijano, JC and Orr, C and Ghannoum, M and Kandeel, F and Husseiny, MI}, title = {Changes in the gut microbiota of NOD mice in response to an oral Salmonella-based vaccine against type 1 diabetes.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0285905}, doi = {10.1371/journal.pone.0285905}, pmid = {37224176}, issn = {1932-6203}, abstract = {We developed an oral Salmonella-based vaccine that prevents and reverses diabetes in non-obese diabetic (NOD) mice. Related to this, the gastrointestinal tract harbors a complex dynamic population of microorganisms, the gut microbiome, that influences host homeostasis and metabolism. Changes in the gut microbiome are associated with insulin dysfunction and type 1 diabetes (T1D). Oral administration of diabetic autoantigens as a vaccine can restore immune balance. However, it was not known if a Salmonella-based vaccine would impact the gut microbiome. We administered a Salmonella-based vaccine to prediabetic NOD mice. Changes in the gut microbiota and associated metabolome were assessed using next-generation sequencing and gas chromatography-mass spectrometry (GC-MS). The Salmonella-based vaccine did not cause significant changes in the gut microbiota composition immediately after vaccination although at 30 days post-vaccination changes were seen. Additionally, no changes were noted in the fecal mycobiome between vaccine- and control/vehicle-treated mice. Significant changes in metabolic pathways related to inflammation and proliferation were found after vaccine administration. The results from this study suggest that an oral Salmonella-based vaccine alters the gut microbiome and metabolome towards a more tolerant composition. These results support the use of orally administered Salmonella-based vaccines that induced tolerance after administration.}, }
@article {pmid37224131, year = {2023}, author = {Jemimah, S and Chabib, CMM and Hadjileontiadis, L and AlShehhi, A}, title = {Gut microbiome dysbiosis in Alzheimer's disease and mild cognitive impairment: A systematic review and meta-analysis.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0285346}, doi = {10.1371/journal.pone.0285346}, pmid = {37224131}, issn = {1932-6203}, abstract = {BACKGROUND: Alzheimer's disease (AD) is a neurodegenerative disorder that causes gradual memory loss. AD and its prodromal stage of mild cognitive impairment (MCI) are marked by significant gut microbiome perturbations, also known as gut dysbiosis. However, the direction and extent of gut dysbiosis have not been elucidated. Therefore, we performed a meta-analysis and systematic review of 16S gut microbiome studies to gain insights into gut dysbiosis in AD and MCI.<br><br>METHODS: We searched MEDLINE, Scopus, EMBASE, EBSCO, and Cochrane for AD gut microbiome studies published between Jan 1, 2010 and Mar 31, 2022. This study has two outcomes: primary and secondary. The primary outcomes explored the changes in &#x3b1;-diversity and relative abundance of microbial taxa, which were analyzed using a variance-weighted random-effects model. The secondary outcomes focused on qualitatively summarized &#x3b2;-diversity ordination and linear discriminant analysis effect sizes. The risk of bias was assessed using a methodology appropriate for the included case-control studies. The geographic cohorts' heterogeneity was examined using subgroup meta-analyses if sufficient studies reported the outcome. The study protocol has been registered with PROSPERO (CRD42022328141).<br><br>FINDINGS: Seventeen studies with 679 AD and MCI patients and 632 controls were identified and analyzed. The cohort is 61.9% female with a mean age of 71.3&#xb1;6.9 years. The meta-analysis shows an overall decrease in species richness in the AD gut microbiome. However, the phylum Bacteroides is consistently higher in US cohorts (standardised mean difference [SMD] 0.75, 95% confidence interval [CI] 0.37 to 1.13, p < 0.01) and lower in Chinese cohorts (SMD -0.79, 95% CI -1.32 to -0.25, p < 0.01). Moreover, the Phascolarctobacterium genus is shown to increase significantly, but only during the MCI stage.<br><br>DISCUSSION: Notwithstanding possible confounding from polypharmacy, our findings show the relevance of diet and lifestyle in AD pathophysiology. Our study presents evidence for region-specific changes in abundance of Bacteroides, a major constituent of the microbiome. Moreover, the increase in Phascolarctobacterium and the decrease in Bacteroides in MCI subjects shows that gut microbiome dysbiosis is initiated in the prodromal stage. Therefore, studies of the gut microbiome can facilitate early diagnosis and intervention in Alzheimer's disease and perhaps other neurodegenerative disorders.}, }
@article {pmid37223817, year = {2023}, author = {Huang, Q and Wang, N and Liu, J and Liao, H and Zeng, Z and Hu, C and Wei, C and Tan, S and Liu, F and Li, G and Huang, H and Chen, D and Wei, S and Qin, Z}, title = {Soil bacterial communities associated with marbled fruit in Citrus reticulata Blanco 'Orah'.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1098042}, pmid = {37223817}, issn = {1664-462X}, abstract = {Citrus reticulata Blanco 'Orah' is grown throughout southern China and provides enormous economic value. However, the agricultural industry has suffered substantial losses during recent years due to marbled fruit disease. The present study focuses on the soil bacterial communities associated with marbled fruit in 'Orah'. The agronomic traits and microbiomes of plants with normal and marbled fruit from three different orchards were compared. No significant differences were found in agronomic traits between the groups, except for higher fruit yields and higher quality of fruits in normal fruit group. Additionally, a total of 2,106,050 16S rRNA gene sequences were generated via the NovoSeq 6000. The alpha diversity index (including the Shannon and Simpson indices), Bray-Curtis similarity, and principal component analyses indicated no significant differences in microbiome diversity between normal and marbled fruit groups. For the healthy 'Orah', the most abundant associated phyla were Bacteroidetes, Firmicutes, and Proteobacteria. In comparison, Burkholderiaceae and Acidobacteria were the most abundant taxa with the marbled fruit group. In addition, the family Xanthomonadaceae and the genus Candidatus Nitrosotalea were prevalent with this group. Analysis using the Kyoto Encyclopedia of Genes and Genomes pathways showed that several pathways related to metabolism significantly differed between the groups. Thus, the present study provides valuable information regarding soil bacterial communities associated with marbled fruit in 'Orah'.}, }
@article {pmid37223726, year = {2023}, author = {Wimmer, BH and Moraïs, S and Zalk, R and Mizrahi, I and Medalia, O}, title = {Phylogenetic diversity of core rumen microbiota as described by cryo-ET.}, journal = {microLife}, volume = {4}, number = {}, pages = {uqad010}, pmid = {37223726}, issn = {2633-6693}, abstract = {Microbial taxonomy is critical for describing ecosystem composition, yet the link between taxonomy and properties of microbes, such as their cellular architecture, remains poorly defined. We hypothesized that the cellular architecture represents microbial niche adaptation. We used cryo-electron microscopy and tomography to analyze microbial morphology in order to associate cellular architecture with phylogeny and genomic contents. As a model system, we chose the core rumen microbiome and imaged a large isolate collection covering 90% of its richness at the order level. Based on quantifications of several morphological features, we found that the visual similarity of microbiota is significantly related to their phylogenetic distance. Up to the Family level, closely related microbes have similar cellular architectures, which are highly correlated with genome similarity. However, in more distantly related bacteria, the correlation both with taxonomy and genome similarity is lost. This is the first comprehensive study of microbial cellular architecture and our results highlight that structure remains an important parameter in classification of microorganisms, along with functional parameters such as metabolomics. Furthermore, the high-quality images presented in this study represent a reference database for the identification of bacteria in anaerobic ecosystems.}, }
@article {pmid37223365, year = {2023}, author = {Katrib, M and Haddad, R and Hamdan, Z and Rida, MA}, title = {The dynamic relationship of gut microbiota with sex hormones in systemic lupus erythematosus.}, journal = {Reumatologia}, volume = {61}, number = {2}, pages = {130-136}, pmid = {37223365}, issn = {0034-6233}, abstract = {Systemic lupus erythematosus (SLE) is a multifactorial autoimmune disease. The sex hormones estrogen and testosterone may have an influence on the production of antibodies. In addition, the gut microbiota also shows an effect on the onset and progression of SLE. Hence, the molecular interplay between sex hormones in terms of gender difference, gut microbiota and SLE is being clarified day after day. The aim of this review is to investigate the dynamic relationship of the gut microbiota with sex hormones in systemic lupus erythematosus taking into account the bacterial strains shown to be affected, effects of antibiotics and other factors that affect the gut microbiome, which itself strongly affects the pathogenesis of SLE.}, }
@article {pmid37223362, year = {2022}, author = {Holst, AQ and Jois, H and Laursen, MF and Sommer, MOA and Licht, TR and Bahl, MI}, title = {Human milk oligosaccharides induce acute yet reversible compositional changes in the gut microbiota of conventional mice linked to a reduction of butyrate levels.}, journal = {microLife}, volume = {3}, number = {}, pages = {uqac006}, pmid = {37223362}, issn = {2633-6693}, abstract = {Human Milk Oligosaccharides (HMOs) are glycans with prebiotic properties known to drive microbial selection in the infant gut, which in turn influences immune development and future health. Bifidobacteria are specialized in HMO degradation and frequently dominate the gut microbiota of breastfed infants. However, some species of Bacteroidaceae also degrade HMOs, which may prompt selection also of these species in the gut microbiota. To investigate to what extent specific HMOs affect the abundance of naturally occurring Bacteroidaceae species in a complex mammalian gut environment, we conducted a study in 40 female NMRI mice administered three structurally different HMOs, namely 6'sialyllactose (6'SL, n = 8), 3-fucosyllactose (3FL, n = 16), and Lacto-N-Tetraose (LNT, n = 8), through drinking water (5%). Compared to a control group receiving unsupplemented drinking water (n = 8), supplementation with each of the HMOs significantly increased both the absolute and relative abundance of Bacteroidaceae species in faecal samples and affected the overall microbial composition analyzed by 16s rRNA amplicon sequencing. The compositional differences were mainly attributed to an increase in the relative abundance of the genus Phocaeicola (formerly Bacteroides) and a concomitant decrease of the genus Lacrimispora (formerly Clostridium XIVa cluster). During a 1-week washout period performed specifically for the 3FL group, this effect was reversed. Short-chain fatty acid analysis of faecal water revealed a decrease in acetate, butyrate and isobutyrate levels in animals supplemented with 3FL, which may reflect the observed decrease in the Lacrimispora genus. This study highlights HMO-driven Bacteroidaceae selection in the gut environment, which may cause a reduction of butyrate-producing clostridia.}, }
@article {pmid37223351, year = {2022}, author = {Homberger, C and Barquist, L and Vogel, J}, title = {Ushering in a new era of single-cell transcriptomics in bacteria.}, journal = {microLife}, volume = {3}, number = {}, pages = {uqac020}, pmid = {37223351}, issn = {2633-6693}, abstract = {Transcriptome analysis of individual cells by single-cell RNA-seq (scRNA-seq) has become routine for eukaryotic tissues, even being applied to whole multicellular organisms. In contrast, developing methods to read the transcriptome of single bacterial cells has proven more challenging, despite a general perception of bacteria as much simpler than eukaryotes. Bacterial cells are harder to lyse, their RNA content is about two orders of magnitude lower than that of eukaryotic cells, and bacterial mRNAs are less stable than their eukaryotic counterparts. Most importantly, bacterial transcripts lack functional poly(A) tails, precluding simple adaptation of popular standard eukaryotic scRNA-seq protocols that come with the double advantage of specific mRNA amplification and concomitant depletion of rRNA. However, thanks to very recent breakthroughs in methodology, bacterial scRNA-seq is now feasible. This short review will discuss recently published bacterial scRNA-seq approaches (MATQ-seq, microSPLiT, and PETRI-seq) and a spatial transcriptomics approach based on multiplexed in situ hybridization (par-seqFISH). Together, these novel approaches will not only enable a new understanding of cell-to-cell variation in bacterial gene expression, they also promise a new microbiology by enabling high-resolution profiling of gene activity in complex microbial consortia such as the microbiome or pathogens as they invade, replicate, and persist in host tissue.}, }
@article {pmid37223092, year = {2023}, author = {Zhou, YJ and Ying, GX and Dong, SL and Xiang, B and Jin, QF}, title = {Gut microbial profile of treatment-naive patients with primary biliary cholangitis.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1126117}, pmid = {37223092}, issn = {1664-3224}, abstract = {BACKGROUND AND AIMS: The pathogenesis of primary biliary cholangitis (PBC) is associated with alterations of gut microbiota. We compared the gut microbiota of PBC patients and healthy controls from Zhejiang Province and assessed the use of these data for the diagnosis of PBC.<br><br>METHODS: First, 16S rRNA gene sequencing was used to characterize the gut microbiota of treatment-naive PBC patients (n=25) and matched healthy controls (n=25). Then, the value of gut microbiota composition for the diagnosis of PBC and assessment of PBC severity was determined.<br><br>RESULTS: The gut microbiota of PBC patients had lower diversity based on three different metrics of alpha-diversity (ace, Chao1, and observed features) and fewer overall genera (all p<0.01). PBC patients had significant enrichment of four genera and significant depletion of eight genera. We identified six amplicon sequence variants (Serratia, Oscillospirales, Ruminococcaceae, Faecalibacterium, Sutterellaceae, and Coprococcus) as optimal biomarkers to distinguish PBC patients from controls based on receiver operating characteristic analysis (area under the curve [AUC] = 0.824). PBC patients who were anti-gp210-positive had lower levels of Oscillospiraceae than those who were anti-gp210-negative. KEGG functional annotation suggested the major changes in the gut microbiota of PBC patients were related to lipid metabolism and biosynthesis of secondary metabolites.<br><br>CONCLUSION: We characterized the gut microbiota of treatment-naive PBC patients and healthy controls from Zhejiang Province. The PBC patients had significant alterations in their gut microbiota, suggesting that gut microbiota composition could be useful as a non-invasive tool for the diagnosis of PBC.}, }
@article {pmid37222987, year = {2023}, author = {Cui, X and Xu, X and Hu, Y and Li, R and Liu, Q}, title = {Mechanism of Qiguiyin Decoction Treats Pulmonary Infection Caused by Pseudomonas aeruginosa Based on Gut Microbiota and Metabolomics.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {3073-3084}, pmid = {37222987}, issn = {1178-6973}, abstract = {BACKGROUND: Qiguiyin decoction (QGYD) was a traditional Chinese medicine (TCM) used to treat Pseudomonas aeruginosa infection in China. This study investigated the therapeutic effect and the potential mechanism of QGYD on carbapenem-resistant Pseudomonas aeruginosa (CRPA) infection.<br><br>MATERIALS AND METHODS: Pulmonary infections were induced in mice by CRPA. The therapeutic effect of QGYD was evaluated by lung index and pulmonary pathology. The potential effects of QGYD on intestinal flora were detected by gut microbiome. The overall metabolism regulation of QGYD in blood was investigated by metabonomics. Next, the correlation between intestinal flora and metabolites was analyzed to illustrate the relationship between the regulatory effects of QGYD on metabolites and the beneficial effects of intestinal flora.<br><br>RESULTS: QGYD has significant therapeutic effect on CRPA infection. QGYD profoundly inhibited the excessive accumulation of Deferribacteres and Mucispirillum at phylum and genus levels, respectively. Eleven potential metabolites that were abnormally expressed by CRPA infection and significantly reversed by QGYD were identified. Ten of the eleven metabolites significantly regulated by QGYD were related to Deferribacteres. Deferribacteres showed significant positive correlation with DL-lactic acid, phenylalanine and other metabolites and significant negative correlation with vitamin k1. At the genus level, Mucispirillum was closely related to metabolites significantly regulated by QGYD. Mucispirillum was positively correlated with metabolites such as Dl-lactate and negatively correlated with vitamin k1.<br><br>CONCLUSION: QGYD can improve CRPA infection and has the effect of regulating intestinal flora and metabolism. It was a promising drug against infection.}, }
@article {pmid37222909, year = {2023}, author = {Schmiedová, L and Černá, K and Li, T and Těšický, M and Kreisinger, J and Vinkler, M}, title = {Bacterial communities along parrot digestive and respiratory tracts: the effects of sample type, species and time.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {37222909}, issn = {1618-1905}, abstract = {Digestive and respiratory tracts are inhabited by rich bacterial communities that can vary between their different segments. In comparison with other bird taxa with developed caeca, parrots that lack caeca have relatively lower variability in intestinal morphology. Here, based on 16S rRNA metabarcoding, we describe variation in microbiota across different parts of parrot digestive and respiratory tracts both at interspecies and intraspecies levels. In domesticated budgerigar (Melopsittacus undulatus), we describe the bacterial variation across eight selected sections of respiratory and digestive tracts, and three non-destructively collected sample types (faeces, and cloacal and oral swabs). Our results show important microbiota divergence between the upper and lower digestive tract, but similarities between respiratory tract and crop, and also between different intestinal segments. Faecal samples appear to provide a better proxy for intestinal microbiota composition than the cloacal swabs. Oral swabs had a similar bacterial composition as the crop and trachea. For a subset of tissues, we confirmed the same pattern also in six different parrot species. Finally, using the faeces and oral swabs in budgerigars, we revealed high oral, but low faecal microbiota stability during a 3-week period mimicking pre-experiment acclimation. Our findings provide a basis essential for microbiota-related experimental planning and result generalisation in non-poultry birds.}, }
@article {pmid37222806, year = {2023}, author = {Korpita, TM and Muths, EL and Watry, MK and McKenzie, VJ}, title = {Captivity, Reintroductions, and the Rewilding of Amphibian-associated Bacterial Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37222806}, issn = {1432-184X}, abstract = {Many studies have noted differences in microbes associated with animals reared in captivity compared to their wild counterparts, but few studies have examined how microbes change when animals are reintroduced to the wild after captive rearing. As captive assurance populations and reintroduction programs increase, a better understanding of how microbial symbionts respond during animal translocations is critical. We examined changes in microbes associated with boreal toads (Anaxyrus boreas), a threatened amphibian, after reintroduction to the wild following captive rearing. Previous studies demonstrate that developmental life stage is an important factor in amphibian microbiomes. We collected 16S marker-gene sequencing datasets to investigate: (i) comparisons of the skin, mouth, and fecal bacteria of boreal toads across four developmental life stages in captivity and the wild, (ii) tadpole skin bacteria before and after reintroduction to the wild, and (iii) adult skin bacteria during reintroduction to the wild. We demonstrated that differences occur across skin, fecal, and mouth bacterial communities in captive versus wild boreal toads, and that the degree of difference depends on developmental stage. Skin bacterial communities from captive tadpoles were more similar to their wild counterparts than captive post-metamorphic individuals were to their wild counterparts. When captive-reared tadpoles were introduced to a wild site, their skin bacteria changed rapidly to resemble wild tadpoles. Similarly, the skin bacterial communities of reintroduced adult boreal toads also shifted to resemble those of wild toads. Our results indicate that a clear microbial signature of captivity in amphibians does not persist after release into natural habitat.}, }
@article {pmid37222697, year = {2023}, author = {Kim, BJ and Hanna, MH}, title = {Colorectal cancer in young adults.}, journal = {Journal of surgical oncology}, volume = {127}, number = {8}, pages = {1247-1251}, doi = {10.1002/jso.27320}, pmid = {37222697}, issn = {1096-9098}, abstract = {The incidence of colorectal cancer in young adults (CRCYAs) is increasing globally, and it is now the third leading cause of cancer death among young adults under 50 years old. The rising incidence is attributed to various emerging risk factors such as genetics, lifestyle factors, and microbiome profiles. Delayed diagnosis and more advanced disease presentation contribute to worse outcomes. A multidisciplinary approach to care is crucial to ensure comprehensive and personalized treatment plans for CRCYA.}, }
@article {pmid37222589, year = {2023}, author = {Che, J and Wu, Y and Yang, H and Wang, S and Wu, W and Lyu, L and Wang, X and Li, W}, title = {Root Niches of Blueberry Imprint Increasing Bacterial-Fungal Interkingdom Interactions along the Soil-Rhizosphere-Root Continuum.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0533322}, doi = {10.1128/spectrum.05333-22}, pmid = {37222589}, issn = {2165-0497}, abstract = {Plant root-associated microbiomes play critical roles in promoting plant health, productivity, and tolerance to biotic/abiotic stresses. Blueberry (Vaccinium spp.) is adapted to acidic soils, while the interactions of the root-associated microbiomes in this specific habitat under various root microenvironments remain elusive. Here, we investigated the diversity and community composition of bacterial and fungal communities in various blueberry root niches (bulk soil, rhizosphere soil, and root endosphere). The results showed that blueberry root niches significantly affected root-associated microbiome diversity and community composition compared to those of the three host cultivars. Deterministic processes gradually increased along the soil-rhizosphere-root continuum in both bacterial and fungal communities. The co-occurrence network topological features showed that both bacterial and fungal community complexity and intensive interactions decreased along the soil-rhizosphere-root continuum. Different compartment niches clearly influenced bacterial-fungal interkingdom interactions, which were significantly higher in the rhizosphere, and positive interactions gradually dominated the co-occurrence networks from the bulk soil to the endosphere. The functional predictions showed that rhizosphere bacterial and fungal communities may have higher cellulolysis and saprotrophy capacities, respectively. Collectively, the root niches not only affected microbial diversity and community composition but also enhanced the positive interkingdom interactions between bacterial and fungal communities along the soil-rhizosphere-root continuum. This provides an essential basis for manipulating synthetic microbial communities for sustainable agriculture. IMPORTANCE The blueberry root-associated microbiome plays an essential role in its adaptation to acidic soils and in limiting the uptake of soil nutrients by its poor root system. Studies on the interactions of the root-associated microbiome in the various root niches may deepen our understanding of the beneficial effects in this particular habitat. Our study extended the research on the diversity and composition of microbial communities in different blueberry root compartment niches. Root niches dominated the root-associated microbiome compared to that of the host cultivar, and deterministic processes increased from the bulk soil to the endosphere. In addition, bacterial-fungal interkingdom interactions were significantly higher in the rhizosphere, and those positive interactions progressively dominated the co-occurrence network along the soil-rhizosphere-root continuum. Collectively, root niches dominantly affected the root-associated microbiome and the positive interkingdom interactions increased, potentially providing benefits for the blueberry.}, }
@article {pmid37222583, year = {2023}, author = {Poudel, R and Jumpponen, A and Kennelly, MM and Rivard, C and Gomez-Montano, L and Garrett, KA}, title = {Integration of Phenotypes in Microbiome Networks for Designing Synthetic Communities: a Study of Mycobiomes in the Grafted Tomato System.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0184322}, doi = {10.1128/aem.01843-22}, pmid = {37222583}, issn = {1098-5336}, abstract = {Understanding factors influencing microbial interactions, and designing methods to identify key taxa that are candidates for synthetic communities, or SynComs, are complex challenges for achieving microbiome-based agriculture. Here, we study how grafting and the choice of rootstock influences root-associated fungal communities in a grafted tomato system. We studied three tomato rootstocks (BHN589, RST-04-106, and Maxifort) grafted to a BHN589 scion and profiled the fungal communities in the endosphere and rhizosphere by sequencing the internal transcribed spacer (ITS2). The data provided evidence for a rootstock effect (explaining ~2% of the total captured variation, P < 0.01) on the fungal community. Moreover, the most productive rootstock, Maxifort, supported greater fungal species richness than the other rootstocks or controls. We then constructed a phenotype-operational taxonomic unit (OTU) network analysis (PhONA) using an integrated machine learning and network analysis approach based on fungal OTUs and associated tomato yield as the phenotype. PhONA provides a graphical framework to select a testable and manageable number of OTUs to support microbiome-enhanced agriculture. We identified differentially abundant OTUs specific to each rootstock in both endosphere and rhizosphere compartments. Subsequent analyses using PhONA identified OTUs that were directly associated with tomato fruit yield and others that were indirectly linked to yield through their links to these OTUs. Fungal OTUs that are directly or indirectly linked with tomato yield may represent candidates for synthetic communities to be explored in agricultural systems. IMPORTANCE The realized benefits of microbiome analyses for plant health and disease management are often limited by the lack of methods to select manageable and testable synthetic microbiomes. We evaluated the composition and diversity of root-associated fungal communities from grafted tomatoes. We then constructed a phenotype-OTU network analysis (PhONA) using these linear and network models. By incorporating yield data in the network, PhONA identified OTUs that were directly predictive of tomato yield and others that were indirectly linked to yield through their links to these OTUs. Follow-up functional studies of taxa associated with effective rootstocks, identified using approaches such as PhONA, could support the design of synthetic fungal communities for microbiome-based crop production and disease management. The PhONA framework is flexible for incorporation of other phenotypic data, and the underlying models can readily be generalized to accommodate other microbiome or 'omics data.}, }
@article {pmid37222576, year = {2023}, author = {Wiśniewska, Z and Kołodziejski, P and Pruszyńska-Oszmałek, E and Konieczka, P and Kinsner, M and Górka, P and Flaga, J and Kowalik, K and Hejdysz, M and Kubiś, M and Jarosz, &#x141;S and Ciszewski, A and Kaczmarek, S}, title = {Combination of emulsifier and xylanase in triticale-based broiler chickens diets.}, journal = {Archives of animal nutrition}, volume = {}, number = {}, pages = {1-18}, doi = {10.1080/1745039X.2023.2202591}, pmid = {37222576}, issn = {1477-2817}, abstract = {The current study aimed to investigate the effect of supplementing an emulsifier, xylanase or a combination of both on the growth performance, digestibility of nutrients, microflora activity and intestinal morphology in broiler chickens fed triticale-based diets. A total of 480 one-day-old male Ross 308 broiler chicks were randomly assigned to four dietary treatments: control (CON), control with an added emulsifier (EMU), control with added xylanase (ENZ) and control with emulsifier and xylanase (EMU+ENZ). Xylanase supplemented groups had diminished feed intake (FI) and enhanced body weight gain (BWG) only within the starter period (p ≤ 0.05), while the feed conversion ratio (FCR) in the ENZ and ENZ+EMU groups was lower than CON during the whole experiment period. There was significant ENZ and EMU interaction in apparent metabolisable energy corrected to N equilibrium (AMEN) as well as NDF and DM retention. The viscosity of ileum digesta was the lowest in groups with enzyme addition. Interactions show that caecal galactosidase-α activity was higher in the CON group compared to EMU supplementation, but similar to ENZ and EMU+ENZ (p < 0.05). Activity of glucosidase-α was higher in the CON group related to inclusion of EMU or ENZ alone (p < 0.05) but did not differ from the combined supplementation of EMU+ENZ, whereas the glucosidase-β activity was higher in the CON group compared to all supplemented diets (p < 0.05). Caecal C2 concentration was greater in the CON group than supplemented diets (p < 0.05). The expression of FATP1, PEPT1 and SGLT1 in the ileum was downregulated after emulsifier addition (p ≤ 0.05). The addition of emulsifier and xylanase indicates a mutual effect on broiler chickens' performance and nutrient digestibility in triticale diets with palm oil during the first nutritional period. Additionally, concomitantly additives usage influenced intestinal microbiome activity, as well.}, }
@article {pmid37222404, year = {2023}, author = {Palla, J and Thapa, S and Venkatachalam, A and Runge, JK and Laguna, TA and Luna, RA}, title = {The upper airway microbiome in Hispanic children with cystic fibrosis.}, journal = {Pediatric pulmonology}, volume = {}, number = {}, pages = {}, doi = {10.1002/ppul.26484}, pmid = {37222404}, issn = {1099-0496}, abstract = {BACKGROUND: Hispanic people with cystic fibrosis (CF) have decreased life expectancy and earlier acquisition of Pseudomonas aeruginosa compared to non-Hispanic white individuals with CF. Racial and ethnic differences in the airway microbiome of CF may contribute to known health disparity, but have not been studied. The objective was to describe differences in the upper airway microbial community in Hispanic and non-Hispanic white children with CF.<br><br>METHODS: This prospective, observational cohort study of 59&#xa0;Hispanic and non-Hispanic white children with CF, ages 2-10 years old, was performed at Texas Children's Hospital (TCH) from February 2019 to January 2020. Oropharyngeal swabs were collected from the cohort during clinic visit. Swab samples underwent sequencing (16S V4 rRNA), diversity analysis, and taxonomic profiling. Key demographic and clinical data were collected from the electronic medical record and the CF Foundation Patient Registry (CFFPR). Statistical analysis compared sequencing, demographic, and clinical data.<br><br>RESULTS: We found no significant difference in Shannon diversity or relative abundance of bacterial phyla between Hispanic and non-Hispanic children with CF. However, a low abundant taxa- "uncultured bacterium" belonging to the order Saccharimonadales was significantly higher in Hispanic children (mean relative abundance&#x2009;=&#x2009;0.13%) compared to the non-Hispanic children (0.03%). Hispanic children had increased incidence of P. aeruginosa (p&#x2009;=&#x2009;0.045) compared to non-Hispanic children.<br><br>CONCLUSION: We did not find a significant difference in the airway microbial diversity between Hispanic and non-Hispanic white children with CF. However, we found a greater relative abundance of Saccharimonadales and higher incidence of P. aeruginosa in Hispanic children with CF.}, }
@article {pmid37222268, year = {2023}, author = {Gómez-Pérez, D and Schmid, M and Chaudhry, V and Hu, Y and Velic, A and Maček, B and Ruhe, J and Kemen, A and Kemen, E}, title = {Proteins released into the plant apoplast by the obligate parasitic protist Albugo selectively repress phyllosphere-associated bacteria.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.18995}, pmid = {37222268}, issn = {1469-8137}, abstract = {Biotic and abiotic interactions shape natural microbial communities. The mechanisms behind microbe-microbe interactions, particularly those protein based, are not well understood. We hypothesize that released proteins with antimicrobial activity are a powerful and highly specific toolset to shape and defend plant niches. We have studied Albugo candida, an obligate plant parasite from the protist Oomycota phylum, for its potential to modulate the growth of bacteria through release of antimicrobial proteins into the apoplast. Amplicon sequencing and network analysis of Albugo-infected and uninfected wild Arabidopsis thaliana samples revealed an abundance of negative correlations between Albugo and other phyllosphere microbes. Analysis of the apoplastic proteome of Albugo-colonized leaves combined with machine learning predictors enabled the selection of antimicrobial candidates for heterologous expression and study of their inhibitory function. We found for three candidate proteins selective antimicrobial activity against Gram-positive bacteria isolated from A. thaliana and demonstrate that these inhibited bacteria are precisely important for the stability of the community structure. We could ascribe the antibacterial activity of the candidates to intrinsically disordered regions and positively correlate it with their net charge. This is the first report of protist proteins with antimicrobial activity under apoplastic conditions that therefore are potential biocontrol tools for targeted manipulation of the microbiome.}, }
@article {pmid37222264, year = {2023}, author = {Carr, RM and Li, Y and Chau, L and Friedman, ES and Lee, JJ and Adorini, L and Erickson, M and Zaru, L and Shringarpure, R and MacConell, L and Bittinger, K and Li, H and Wu, GD}, title = {An integrated analysis of fecal microbiome and metabolomic features distinguish Non-cirrhotic NASH from healthy control populations.}, journal = {Hepatology (Baltimore, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1097/HEP.0000000000000474}, pmid = {37222264}, issn = {1527-3350}, abstract = {There is great interest in identifying microbiome features as reliable noninvasive diagnostic and/or prognostic biomarkers for non-cirrhotic NASH fibrosis. Several cross-sectional studies have reported gut microbiome features associated with advanced NASH fibrosis and cirrhosis, where the most prominent features are associated with cirrhosis. However, no large, prospectively collected data exist establishing microbiome features that discern non-cirrhotic NASH fibrosis, integrate the fecal metabolome as disease biomarkers, and are unconfounded by BMI and age. Results from shotgun metagenomic sequencing performed on fecal samples prospectively collected from 279 US patients with biopsy-proven NASH (F1-F3 fibrosis) enrolled in the REGENERATE I303 study were compared to those from three healthy control cohorts and integrated with the absolute quantification of fecal bile acids. Microbiota beta-diversity was different, and BMI- and age-adjusted logistic regression identified 12 NASH-associated species. Random forest prediction models resulted in an AUC of 0.75 to 0.81 in a receiver operator characteristic analysis. Additionally, specific fecal bile acids were significantly lower in NASH and correlated with plasma C4 levels. Microbial gene abundance analysis revealed 127 genes increased in controls, many involving protein synthesis, whereas 362 genes were increased in NASH many involving bacterial environmental responses (FDR < 0.01). Finally, we provide evidence that fecal bile acid levels may be a better discriminator of non-cirrhotic NASH versus health than either plasma bile acids or gut microbiome features. These results may have value as a set of baseline characteristics of non-cirrhotic NASH against which therapeutic interventions to prevent cirrhosis can be compared and microbiome-based diagnostic biomarkers identified.}, }
@article {pmid37222190, year = {2023}, author = {Bruno, JS and Fregnani, ER}, title = {Oral microbiome as a new research-target for supportive care and precision oncology.}, journal = {Current opinion in oncology}, volume = {}, number = {}, pages = {}, doi = {10.1097/CCO.0000000000000947}, pmid = {37222190}, issn = {1531-703X}, abstract = {PURPOSE OF REVIEW: A growing number of studies demonstrate the oral bacterial shift in cancer patients and the enrichment of oral bacteria in distant tumours. During the oncological treatment, opportunistic oral bacteria correlate with oral toxicities. This review focused on the most recent studies to identify which genera are the most mentioned and deserved further investigation.<br><br>RECENT FINDINGS: This review evaluated bacterial changes in patients with head and neck, colorectal, lung and breast cancer. Greater composition of disease-related genera (e.g., Fusobacterium, Porphyromonas, Lactobacillus, Streptococcus, and Parvimonas) are present in the oral cavity of these groups of patients. The tumour specimen characterisation of head and neck, pancreatic and colorectal cancer also describes the presence of oral taxa. No evidence indicates that commensal oral bacteria have protective roles in distant tumours. Regardless, oral care is critical to prevent the growth of oral pathogens and reduce infection foci.<br><br>SUMMARY: Recent evidence suggests that oral microbiota is a potential biomarker for oncological clinical outcomes and oral toxicities. Currently, the literature presents a remarkable methodological variety - from the sample collection site to the preference of the data analysis tools. For the oral microbiome to achieve the stage of being used as a clinical tool in the oncological context, more studies are necessary.}, }
@article {pmid37222188, year = {2023}, author = {Desilets, A and Elkrief, A}, title = {Following your gut: the emerging role of the gut microbiota in predicting and treating immune-related adverse events.}, journal = {Current opinion in oncology}, volume = {}, number = {}, pages = {}, doi = {10.1097/CCO.0000000000000957}, pmid = {37222188}, issn = {1531-703X}, abstract = {PURPOSE OF REVIEW: Although immune checkpoint inhibition has reshaped the therapeutic landscape leading to improved outcomes across an array of both solid and hematologic malignancies, a significant source of morbidity is caused by immune-related adverse events (irAEs) caused by these agents.<br><br>RECENT FINDINGS: The gut microbiota has emerged as a biomarker of response to these agents, and more recently, also as a key determinant of development of irAEs. Emerging data have revealed that enrichment of certain bacterial genera is associated with an increased risk of irAEs, with the most robust evidence pointing to an intimate connection with the development of immune-related diarrhea and colitis. These bacteria include Bacteroides, Enterobacteriaceae, and Proteobacteria (such as Klebsiella and Proteus). Lachnospiraceae spp. and Streptococcus spp. have been implicated irAE-wide in the context of ipilimumab.<br><br>SUMMARY: We review recent lines of evidence pointing to the role of baseline gut microbiota on the development of irAE, and the potentials for therapeutic manipulation of the gut microbiota in order to reduce irAE severity. The connections between gut microbiome signatures of response and toxicity will need to be untangled in further studies.}, }
@article {pmid37222184, year = {2023}, author = {Liu, YH and Zhuo, XJ and Hung, YM and Wang, YH and Chang, R and Wei, JC}, title = {Absence of an association between gastrointestinal tract surgery and newly diagnosed psoriasis: A nationwide, population-based, nested, case-control study.}, journal = {International journal of rheumatic diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/1756-185X.14750}, pmid = {37222184}, issn = {1756-185X}, abstract = {BACKGROUND: Gastrointestinal tract surgeries could disrupt the microbiome and simultaneously cause trauma, which may result in psoriasis.<br><br>OBJECTIVE: To examine associations between gastrointestinal tract surgeries and newly diagnosed psoriasis.<br><br>METHODS: This nested case-control study included patients with newly diagnosed psoriasis from 2005 to 2013, retrieved from the Taiwan National Health Insurance Research Database. We retrospectively (5&#x2009;years from the index date) determined whether the patients had undergone gastrointestinal tract surgery.<br><br>RESULTS: We identified 16&#x2009;655 patients with newly diagnosed psoriasis and matched 33&#x2009;310 individuals as the control group. The population was stratified by age and sex. There was no association between age and psoriasis (<20&#x2009;years: adjusted odds ratio [aOR] 0.80, 95% confidence interval [CI] 0.52-1.24; 20-39&#x2009;years: aOR 1.09, 95% CI 0.79-1.51; 40-59&#x2009;years: aOR 0.89, 95% CI 0.57-1.39; &#x2265;60&#x2009;years: aOR 0.82, 95% CI 0.54-1.26). Similar findings were obtained by sex, with no differences among men (aOR 0.90, 95% CI 0.69-1.17) and women (aOR 0.96, 95% CI 0.71-1.29).<br><br>CONCLUSION: Our study indicates that gastrointestinal surgeries have limited age- and sex-related effects on psoriasis. These findings provide new insights into the risk of developing psoriasis.}, }
@article {pmid37221898, year = {2023}, author = {Koort, K and Sõsa, K and Türk, S and Lapp, E and Talving, E and Karits, P and Rosenstein, K and Jaagura, M and Sekavin, A and Sõritsa, D and Haldre, K and Karro, H and Korrovits, P and Salumets, A and Mändar, R}, title = {Lactobacillus crispatus-dominated vaginal microbiome and Acinetobacter-dominated seminal microbiome support beneficial ART outcome.}, journal = {Acta obstetricia et gynecologica Scandinavica}, volume = {}, number = {}, pages = {}, doi = {10.1111/aogs.14598}, pmid = {37221898}, issn = {1600-0412}, abstract = {INTRODUCTION: Despite the considerable progress made in assisted reproductive technologies (ART), the implantation rate of transferred embryos remains low and in many cases, the reasons for failure remain unclear. We aimed to determine the potential impact of female and male partners' reproductive tract microbiome composition on ART outcome.<br><br>MATERIAL AND METHODS: The ART couples (n&#x2009;=&#x2009;97) and healthy couples (n&#x2009;=&#x2009;12) were recruited into the study. The smaller healthy group underwent a careful selection according to their reproductive and general health criteria. Both vaginal and semen samples were subjected to 16S rDNA sequencing to reveal the bacterial diversity and identify distinct microbial community types. Ethics statement The study was approved by the Ethics Review Committee on Human Research of Tartu University, Tartu, Estonia (protocol no. 193/T-16) on 31 May 2010. Participation in the research was voluntary. Written informed consent was obtained from all study participants.<br><br>RESULTS: The men with Acinetobacter-associated community who had children in the past, had the highest ART success rate (P&#x2009;<&#x2009;0.05). The women with bacterial vaginosis vaginal microbiome community and with L. iners-predominant and L. gasseri-predominant microbiome had a lower ART success rate than women with the L. crispatus-predominant or the mixed lactic-acid-bacteria-predominant type (P&#x2009;<&#x2009;0.05). The 15 couples where both partners had beneficial microbiome types had a superior ART success rate of 53%, when compared with the rest of the couples (25%; P&#x2009;=&#x2009;0.023).<br><br>CONCLUSIONS: Microbiome disturbances in the genital tract of both partners tend to be associated with couple's infertility as well as lower ART success levels and may thus need attention before the ART procedure. The incorporation of genitourinary microbial screening as a part of the diagnostic evaluation process may become routine for ART patients if our results are confirmed by other studies.}, }
@article {pmid37221488, year = {2023}, author = {Li, G and Sun, Y and Huang, Y and Lian, J and Wu, S and Luo, D and Gong, H}, title = {Fusobacterium nucleatum-derived small extracellular vesicles facilitate tumor growth and metastasis via TLR4 in breast cancer.}, journal = {BMC cancer}, volume = {23}, number = {1}, pages = {473}, pmid = {37221488}, issn = {1471-2407}, abstract = {BACKGROUND: The contributive role of the microbiome in tumor progression has been reported in multiple studies, such as the Fusobacterium nucleatum (F. nucleatum) in breast cancer (BC). This study aimed to explore the role of F. nucleatum-derived small extracellular vesicles (Fn-EVs) in BC and preliminarily uncover the mechanism.<br><br>METHODS: Ten normal and 20 cancerous breast tissues were harvested to investigate the gDNA expression of F. nucleatum and its relation with the clinical characteristics of BC patients. After isolating Fn-EVs by ultracentrifugation from F. nucleatum (ATCC 25,586), both MDA-MB-231 and MCF-7 cells were treated with PBS, Fn, or Fn-EVs, followed by being subjected to CCK-8, Edu staining, wound healing, and Transwell assays to detect their cell viability, proliferation, migration, and invasion. TLR4 expression in BC cells with diverse treatments was assessed by western blot. In vivo experiments were performed to verify its role in tumor growth and liver metastasis.<br><br>RESULTS: The F. nucleatum gDNA levels of breast tissues in BC patients were significantly higher than those in normal subjects, and positively associated with tumor size and metastasis. Fn-EVs administration significantly enhanced the cell viability, proliferation, migration, and invasion of BC cells, while knocking down TLR4 in BC cells could block these effects. Furthermore, in vivo study verified the contributive role of Fn-EVs in tumor growth and metastasis of BC, which might rely on its regulation of TLR4.<br><br>CONCLUSIONS: Collectively, our results suggest that F. nucleatum plays an important role in BC tumor growth and metastasis by regulating TLR4 through Fn-EVs. Thus, a better understanding of this process may aid in the development of novel therapeutic agents.}, }
@article {pmid37221274, year = {2023}, author = {Megremis, S and Constantinides, B and Xepapadaki, P and Yap, CF and Sotiropoulos, AG and Bachert, C and Finotto, S and Jartti, T and Tapinos, A and Vuorinen, T and Andreakos, E and Robertson, DL and Papadopoulos, NG}, title = {Respiratory eukaryotic virome expansion and bacteriophage deficiency characterize childhood asthma.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8319}, pmid = {37221274}, issn = {2045-2322}, abstract = {Asthma development and exacerbation is linked to respiratory virus infections. There is limited information regarding the presence of viruses during non-exacerbation/infection periods. We investigated the nasopharyngeal/nasal virome during a period of asymptomatic state, in a subset of 21 healthy and 35 asthmatic preschool children from the Predicta cohort. Using metagenomics, we described the virome ecology and the cross-species interactions within the microbiome. The virome was dominated by eukaryotic viruses, while prokaryotic viruses (bacteriophages) were independently observed with low abundance. Rhinovirus B species consistently dominated the virome in asthma. Anelloviridae were the most abundant and rich family in both health and asthma. However, their richness and alpha diversity were increased in asthma, along with the co-occurrence of different Anellovirus genera. Bacteriophages were richer and more diverse in healthy individuals. Unsupervised clustering identified three virome profiles that were correlated to asthma severity and control and were independent of treatment, suggesting a link between the respiratory virome and asthma. Finally, we observed different cross-species ecological associations in the healthy versus the asthmatic virus-bacterial interactome, and an expanded interactome of eukaryotic viruses in asthma. Upper respiratory virome "dysbiosis" appears to be a novel feature of pre-school asthma during asymptomatic/non-infectious states and merits further investigation.}, }
@article {pmid37221272, year = {2023}, author = {Hsia, K and Zhao, N and Chung, M and Algarrahi, K and Kouhsari, LM and Fu, M and Chen, H and Singh, S and Michaud, DS and Jangi, S}, title = {Alterations in the Fungal Microbiome in Ulcerative Colitis.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izad082}, pmid = {37221272}, issn = {1536-4844}, support = {KL2TR002545/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: Although gut fungi have been implicated in the immunopathogenesis of inflammatory bowel disease, the fungal microbiome has not been deeply explored across endohistologic activity and treatment exposure in ulcerative colitis.<br><br>METHODS: We analyzed data from the SPARC IBD (Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease) registry. We evaluated the fungal composition of fecal samples from 98 patients with ulcerative colitis across endoscopic activity (n&#x2005;=&#x2005;43), endohistologic activity (n&#x2005;=&#x2005;41), and biologic exposure (n&#x2005;=&#x2005;82). Across all subgroups, we assessed fungal diversity and differential abundance of taxonomic groups.<br><br>RESULTS: We identified 500 unique fungal amplicon sequence variants across the cohort of 82 patients, dominated by phylum Ascomycota. Compared with endoscopic remission, patients with endoscopic activity had increased Saccharomyces (log2 fold change = 4.54; adjusted P&#x2005;<&#x2005;5&#x2005;&#xd7;&#x2005;10-5) and increased Candida (log2 fold change = 2.56; adjusted P&#x2005;<&#x2005;.03). After adjusting for age, sex, and biologic exposure among patients with endoscopic activity, Saccharomyces (log2 fold change = 7.76; adjusted P <&#x2005;1&#x2005;&#xd7;&#x2005;10-15) and Candida (log2 fold change = 7.28; adjusted P<&#x2005;1&#x2005;&#xd7;&#x2005;10-8) remained enriched during endoscopic activity compared with quiescence.<br><br>CONCLUSIONS: Endoscopic inflammation in ulcerative colitis is associated with an expansion of Saccharomyces and Candida compared with remission. The role of these fungal taxa as potential biomarkers and targets for personalized approaches to therapeutics in ulcerative colitis should be evaluated.}, }
@article {pmid37221166, year = {2023}, author = {Dekkers, KF and Sayols-Baixeras, S and Baldanzi, G and Nowak, C and Hammar, U and Nguyen, D and Varotsis, G and Brunkwall, L and Nielsen, N and Eklund, AC and Bak Holm, J and Nielsen, HB and Ottosson, F and Lin, YT and Ahmad, S and Lind, L and Sundström, J and Engström, G and Smith, JG and Ärnlöv, J and Orho-Melander, M and Fall, T}, title = {Author Correction: An online atlas of human plasma metabolite signatures of gut microbiome composition.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {2971}, doi = {10.1038/s41467-023-38607-1}, pmid = {37221166}, issn = {2041-1723}, }
@article {pmid37221143, year = {2023}, author = {Vahidi, G and Moody, M and Welhaven, HD and Davidson, L and Rezaee, T and Behzad, R and Karim, L and Roggenbeck, BA and Walk, ST and Martin, SA and June, RK and Heveran, CM}, title = {Germ-free C57BL/6 mice have increased bone mass and altered matrix properties but not decreased bone fracture resistance.}, journal = {Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research}, volume = {}, number = {}, pages = {}, doi = {10.1002/jbmr.4835}, pmid = {37221143}, issn = {1523-4681}, abstract = {The gut microbiome impacts bone mass, which implies a disruption to bone homeostasis. However, it is not yet clear how the gut microbiome affects the regulation of bone mass and bone quality. We hypothesized that germ-free (GF) mice have increased bone mass and decreased bone toughness compared with conventionally-housed mice. We tested this hypothesis using adult (20 to 21-week-old) C57BL/6J GF and conventionally-raised female and male mice (n=6-10/group). Trabecular microarchitecture and cortical geometry were measured from microCT of the femur distal metaphysis and cortical midshaft. Whole-femur strength and estimated material properties were measured using three-point bending and notched fracture toughness. Bone matrix properties were measured for the cortical femur by quantitative backscattered electron imaging, nanoindentation, Raman spectroscopy, and for the humerus by fluorescent advanced glycation end-product assay (fAGEs). Shifts in cortical tissue metabolism were measured from the contralateral humerus. GF mice had reduced bone resorption, increased trabecular bone microarchitecture, increased tissue strength that was not explained by differences in bone size, increased tissue mineralization and fAGEs, and altered collagen structure that did not decrease fracture toughness. We observed several sex differences in GF mice, most notably for bone tissue metabolism. Male GF mice had a greater signature of amino acid metabolism and female GF mice had a greater signature of lipid metabolism, exceeding the metabolic sex differences of the conventional mice. Together, these data demonstrate that the GF state in C57BL/6J mice alters bone mass and matrix properties but does not decrease bone fracture resistance.}, }
@article {pmid37220909, year = {2023}, author = {Jeong, SM and Jin, EJ and Wei, S and Bae, JH and Ji, Y and Jo, Y and Jeong, JH and Im, SJ and Ryu, D}, title = {The impact of cancer cachexia on gut microbiota composition and short-chain fatty acid metabolism in a murine model.}, journal = {BMB reports}, volume = {}, number = {}, pages = {}, pmid = {37220909}, issn = {1976-670X}, abstract = {This study investigates the relationship between cancer cachexia and the gut microbiota, focusing on the influence of cancer on microbial composition. Lewis lung cancer cell allografts were used to induce cachexia in mice, and body and muscle weight changes were monitored. Fecal samples were collected for targeted metabolomic analysis for short chain fatty acids and microbiome analysis. The cachexia group exhibited lower alpha diversity and distinct beta diversity in gut microbiota compared to the control group. Differential abundance analysis revealed higher Bifidobacterium and Romboutsia, but lower Streptococcus abundance in the cachexia group. Additionally, lower proportions of acetate and butyrate were observed in the cachexia group. The study observed that a significant impact of cancer cachexia on gut microbiota and their generated metabolites, indicating the host-to-gut microbiota axis.}, }
@article {pmid37220834, year = {2023}, author = {Zhang, JS and Chen, Z and Chu, CH and Yu, OY}, title = {Effect of silver diamine fluoride upon the microbial community of carious lesions: A scoping review.}, journal = {Journal of dentistry}, volume = {}, number = {}, pages = {104554}, doi = {10.1016/j.jdent.2023.104554}, pmid = {37220834}, issn = {1879-176X}, abstract = {OBJECTIVES: To explore the effects of silver diamine fluoride (SDF) on the microbial community of carious lesions.<br><br>DATA: Original studies evaluating the effect of SDF treatment on the microbial community of human carious lesions were included.<br><br>SOURCES: A systematic search of English-language publications was performed in PubMed, EMBASE, Scopus, and Web of Science. Gray literature was searched in ClinicalTrials.gov and Google Scholar.<br><br>STUDY SELECTION/RESULTS: This review included seven publications reporting the effects of SDF on microbial community of dental plaque or carious dentin, including the microbial biodiversity, relative abundance of microbial taxa, and predicted functional pathways of the microbial community. The studies on microbial community of dental plaque reported that SDF did not have a significant effect on both the within-community species diversity (alpha-diversity) and inter-community microbial compositional dissimilarity (beta-diversity) of the plaque microbial communities. However, SDF changed the relative abundance of 29 bacterial species of plaque community, inhibited carbohydrate transportation and interfered with the metabolic functions of the plaque microbial community. A study on the microbial community in dentin carious lesions reported that SDF affected its beta-diversity and changed the relative abundance of 14 bacterial species.<br><br>CONCLUSION: SDF showed no significant effects on the biodiversity of the plaque microbial community but changed the beta-diversity of the carious dentin microbial community. SDF could change the relative abundance of certain bacterial species in the dental plaque and the carious dentin. SDF could also affect the predicted functional pathways of the microbial community.<br><br>CLINICAL SIGNIFICANCE: This review provided comprehensive evidence on the potential effect of SDF treatment on the microbial community of carious lesions.}, }
@article {pmid37220806, year = {2023}, author = {Pinjari, OF and Jones, GH and Vecera, CM and Smith, K and Barrera, A and Machado-Vieira, R}, title = {The Role of the Gut Microbiome in Bipolar Disorder and its Common Comorbidities.}, journal = {Frontiers in neuroendocrinology}, volume = {}, number = {}, pages = {101078}, doi = {10.1016/j.yfrne.2023.101078}, pmid = {37220806}, issn = {1095-6808}, abstract = {Bipolar disorder is a decidedly heterogeneous and multifactorial disease, with significant psychosocial and medical disease burden. Much difficulty has been encountered in developing novel therapeutics and objective biomarkers for clinical use in this population. In that regard, gut-microbial homeostasis appears to modulate several key pathways relevant to a variety of psychiatric, metabolic, and inflammatory disorders. Microbial impact on immune, endocrine, endocannabinoid, kynurenine, and other pathways are discussed throughout this review. Emphasis is placed on this system's relevance to current pharmacology, diet, and comorbid illness in bipolar disorder. Despite the high level of optimism promoted in many reviews on this topic, substantial obstacles exist before any microbiome-related findings can provide meaningful clinical utility. Beyond a comprehensive overview of pathophysiology, this review hopes to highlight several key areas where progress is needed. As well, novel microbiome-associated suggestions are presented for future research.}, }
@article {pmid37220524, year = {2023}, author = {Dong, Y and Xu, R and Chen, X and Yang, C and Jiang, F and Shen, Y and Li, Q and Fang, F and Li, Y and Shen, X}, title = {Characterization of gut microbiota in adults with coronary atherosclerosis.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15245}, pmid = {37220524}, issn = {2167-8359}, abstract = {BACKGROUND: Cardiovascular disease, which is mainly caused by coronary atherosclerosis, is one of the leading causes of death and disability worldwide. Gut microbiota likely play an important role in coronary atherosclerosis. This study aims to investigate the microbiota profile of adults with coronary atherosclerosis to provide a theoretical basis for future research.<br><br>METHODS: Fecal samples were collected from 35 adult patients diagnosed with coronary atherosclerosis and 32 healthy adults in Nanjing, China, and the V3-V4 region of 16S rDNA genes was sequenced using high-throughput sequencing. Differences in alpha diversity, beta diversity, and gut microbiota composition between the two groups were then compared.<br><br>RESULTS: A beta diversity analysis revealed significant differences between adults with coronary atherosclerosis and controls, but there was no statistical difference in alpha diversity between the two groups. There were also differences in the composition of the gut microbiota between the two groups. The genera, Megamonas, Streptococcus, Veillonella, Ruminococcus_torques_group, Prevotella_2, Tyzzerella_4, were identified as potential biomarkers for coronary atherosclerosis.<br><br>CONCLUSION: There are some differences in the gut microbiota of adults with coronary atherosclerosis compared to healthy adults. The insights from this study could be used to explore microbiome-based mechanisms for coronary atherosclerosis.}, }
@article {pmid37220321, year = {2023}, author = {Vangeenderhuysen, P and Van Arnhem, J and Pomian, B and De Graeve, M and De Commer, L and Falony, G and Raes, J and Zhernakova, A and Fu, J and Hemeryck, LY and Vanhaecke, L}, title = {Dual UHPLC-HRMS Metabolomics and Lipidomics and Automated Data Processing Workflow for Comprehensive High-Throughput Gut Phenotyping.}, journal = {Analytical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.analchem.2c05371}, pmid = {37220321}, issn = {1520-6882}, abstract = {In recent years, feces has surfaced as the matrix of choice for investigating the gut microbiome-health axis because of its non-invasive sampling and the unique reflection it offers of an individual's lifestyle. In cohort studies where the number of samples required is large, but availability is scarce, a clear need exists for high-throughput analyses. Such analyses should combine a wide physicochemical range of molecules with a minimal amount of sample and resources and downstream data processing workflows that are as automated and time efficient as possible. We present a dual fecal extraction and ultra high performance liquid chromatography-high resolution-quadrupole-orbitrap-mass spectrometry (UHPLC-HR-Q-Orbitrap-MS)-based workflow that enables widely targeted and untargeted metabolome and lipidome analysis. A total of 836 in-house standards were analyzed, of which 360 metabolites and 132 lipids were consequently detected in feces. Their targeted profiling was validated successfully with respect to repeatability (78% CV < 20%), reproducibility (82% CV < 20%), and linearity (81% R[2] > 0.9), while also enabling holistic untargeted fingerprinting (15,319 features, CV < 30%). To automate targeted processing, we optimized an R-based targeted peak extraction (TaPEx) algorithm relying on a database comprising retention time and mass-to-charge ratio (360 metabolites and 132 lipids), with batch-specific quality control curation. The latter was benchmarked toward vendor-specific targeted and untargeted software and our isotopologue parameter optimization/XCMS-based untargeted pipeline in LifeLines Deep cohort samples (n = 97). TaPEx clearly outperformed the untargeted approaches (81.3 vs 56.7-66.0% compounds detected). Finally, our novel dual fecal metabolomics-lipidomics-TaPEx method was successfully applied to Flemish Gut Flora Project cohort (n = 292) samples, leading to a sample-to-result time reduction of 60%.}, }
@article {pmid37220256, year = {2023}, author = {Amrofell, MB and Moon, TS}, title = {Characterizing a Propionate Sensor in E. coli Nissle 1917.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.3c00138}, pmid = {37220256}, issn = {2161-5063}, abstract = {Short-chain fatty acids (SCFAs) are commonly found in the large intestine, but generally not in the small intestine, and influence microbiome composition and host physiology. Thus, synthetic biologists are interested in developing engineered probiotics capable of in situ detection of SCFAs as biogeography or disease sensors. One SCFA, propionate, is both sensed and consumed by E. coli. Here, we utilize the E. coli transcription factor PrpR, sensitive to the propionate-derived metabolite (2S,3S)-2-methylcitrate, and its cognate promoter PprpBCDE to detect extracellular propionate with the probiotic chassis bacterium E. coli Nissle 1917. We identify that PrpR-PprpBCDE displays stationary phase leakiness and transient bimodality, and we explain these observations through evolutionary rationales and deterministic modeling, respectively. Our results will help researchers build biogeographically sensitive genetic circuits.}, }
@article {pmid37223356, year = {2022}, author = {Rigou, S and Christo-Foroux, E and Santini, S and Goncharov, A and Strauss, J and Grosse, G and Fedorov, AN and Labadie, K and Abergel, C and Claverie, JM}, title = {Metagenomic survey of the microbiome of ancient Siberian permafrost and modern Kamchatkan cryosols.}, journal = {microLife}, volume = {3}, number = {}, pages = {uqac003}, pmid = {37223356}, issn = {2633-6693}, abstract = {In the context of global warming, the melting of Arctic permafrost raises the threat of a reemergence of microorganisms some of which were shown to remain viable in ancient frozen soils for up to half a million years. In order to evaluate this risk, it is of interest to acquire a better knowledge of the composition of the microbial communities found in this understudied environment. Here, we present a metagenomic analysis of 12 soil samples from Russian Arctic and subarctic pristine areas: Chukotka, Yakutia and Kamchatka, including nine permafrost samples collected at various depths. These large datasets (9.2 × 10[11] total bp) were assembled (525 313 contigs > 5 kb), their encoded protein contents predicted, and then used to perform taxonomical assignments of bacterial, archaeal and eukaryotic organisms, as well as DNA viruses. The various samples exhibited variable DNA contents and highly diverse taxonomic profiles showing no obvious relationship with their locations, depths or deposit ages. Bacteria represented the largely dominant DNA fraction (95%) in all samples, followed by archaea (3.2%), surprisingly little eukaryotes (0.5%), and viruses (0.4%). Although no common taxonomic pattern was identified, the samples shared unexpected high frequencies of β-lactamase genes, almost 0.9 copy/bacterial genome. In addition to known environmental threats, the particularly intense warming of the Arctic might thus enhance the spread of bacterial antibiotic resistances, today's major challenge in public health. β-Lactamases were also observed at high frequency in other types of soils, suggesting their general role in the regulation of bacterial populations.}, }
@article {pmid37223256, year = {2021}, author = {Du, X and Ley, R and Buck, AH}, title = {MicroRNAs and extracellular vesicles in the gut: new host modulators of the microbiome?.}, journal = {microLife}, volume = {2}, number = {}, pages = {uqab010}, pmid = {37223256}, issn = {2633-6693}, abstract = {The gut microbiota plays an integral role in human health and its dysbiosis is associated with many chronic diseases. There are still large gaps in understanding the host and environmental factors that directly regulate the gut microbiota, and few effective strategies exist to modulate the microbiota in therapeutic applications. Recent reports suggest that certain microRNAs (miRNAs) released by mammalian cells can regulate bacterial gene expression to influence the microbiome composition and propose extracellular vesicles as one natural mechanism for miRNA transport in the gut. These new findings interface with a burgeoning body of data showing that miRNAs are present in a stable form in extracellular environments and can mediate cell-to-cell communication in mammals. Here, we review the literature on RNA-mediated modulation of the microbiome to bring cross-disciplinary perspective to this new type of interaction and its potential implications in biology and medicine.}, }
@article {pmid37220079, year = {2023}, author = {DiBello, M and Healy, AR and Nikolayevskiy, H and Xu, Z and Herzon, SB}, title = {Structure Elucidation of Secondary Metabolites: Current Frontiers and Lingering Pitfalls.}, journal = {Accounts of chemical research}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.accounts.3c00183}, pmid = {37220079}, issn = {1520-4898}, abstract = {ConspectusAnalytical methods allow for the structure determination of submilligram quantities of complex secondary metabolites. This has been driven in large part by advances in NMR spectroscopic capabilities, including access to high-field magnets equipped with cryogenic probes. Experimental NMR spectroscopy may now be complemented by remarkably accurate carbon-13 NMR calculations using state-of-the-art DFT software packages. Additionally, microED analysis stands to have a profound effect on structure elucidation by providing X-ray-like images of microcrystalline samples of analytes. Nonetheless, lingering pitfalls in structure elucidation remain, particularly for isolates that are unstable or highly oxidized. In this Account, we discuss three projects from our laboratory that highlight nonoverlapping challenges to the field, with implications for chemical, synthetic, and mechanism of action studies. We first discuss the lomaiviticins, complex unsaturated polyketide natural products disclosed in 2001. The original structures were derived from NMR, HRMS, UV-vis, and IR analysis. Owing to the synthetic challenges presented by their structures and the absence of X-ray crystallographic data, the structure assignments remained untested for nearly two decades. In 2021, the Nelson group at Caltech carried out microED analysis of (-)-lomaiviticin C, leading to the startling discovery that the original structure assignment of the lomaiviticins was incorrect. Acquisition of higher-field (800 MHz [1]H, cold probe) NMR data as well as DFT calculations provided insights into the basis for the original misassignment and lent further support to the new structure identified by microED. Reanalysis of the 2001 data set reveals that the two structure assignments are nearly indistinguishable, underscoring the limitations of NMR-based characterization. We then discuss the structure elucidation of colibactin, a complex, nonisolable microbiome metabolite implicated in colorectal cancer. The colibactin biosynthetic gene cluster was detected in 2006, but owing to colibactin's instability and low levels of production, it could not be isolated or characterized. We used a combination of chemical synthesis, mechanism of action studies, and biosynthetic analysis to identify the substructures in colibactin. These studies, coupled with isotope labeling and tandem MS analysis of colibactin-derived DNA interstrand cross-links, ultimately led to a structure assignment for the metabolite. We then discuss the ocimicides, plant secondary metabolites that were studied as agents against drug-resistant P. falciparum. We synthesized the core structure of the ocimicides and found significant discrepancies between our experimental NMR spectroscopic data and that reported for the natural products. We determined the theoretical carbon-13 NMR shifts for 32 diastereomers of the ocimicides. These studies indicated that a revision of the connectivity of the metabolites is likely needed. We end with some thoughts on the frontiers of secondary metabolite structure determination. As modern NMR computational methods are straightforward to execute, we advocate for their systematic use in validating the assignments of novel secondary metabolites.}, }
@article {pmid37220071, year = {2023}, author = {Zangara, MT and Darwish, L and Coombes, BK}, title = {Characterizing the Pathogenic Potential of Crohn's Disease-Associated Adherent-Invasive Escherichia coli.}, journal = {EcoSal Plus}, volume = {}, number = {}, pages = {eesp00182022}, pmid = {37220071}, issn = {2324-6200}, abstract = {The microbiome of Crohn's disease (CD) patients is composed of a microbial community that is considered dysbiotic and proinflammatory in nature. The overrepresentation of Enterobacteriaceae species is a common feature of the CD microbiome, and much attention has been given to understanding the pathogenic role this feature plays in disease activity. Over 2 decades ago, a new Escherichia coli subtype called adherent-invasive E. coli (AIEC) was isolated and linked to ileal Crohn's disease. Since the isolation of the first AIEC strain, additional AIEC strains have been isolated from both inflammatory bowel disease (IBD) patients and non-IBD individuals using the original in vitro phenotypic characterization methods. Identification of a definitive molecular marker of the AIEC pathotype has been elusive; however, significant advancements have been made in understanding the genetic, metabolic, and virulence determinants of AIEC infection biology. Here, we review the current knowledge of AIEC pathogenesis to provide additional, objective measures that could be considered in defining AIEC and their pathogenic potential.}, }
@article {pmid37219936, year = {2023}, author = {Luo, Y and Tong, Y and Wu, L and Niu, H and Li, Y and Su, LC and Wu, Y and Bozec, A and Zaiss, MM and Qing, P and Zhao, H and Tan, C and Zhang, Q and Zhao, Y and Tang, H and Liu, Y}, title = {Alteration of gut microbiota in high-risk individuals for rheumatoid arthritis is associated with disturbed metabolome and initiates arthritis by triggering mucosal immunity imbalance.}, journal = {Arthritis &amp; rheumatology (Hoboken, N.J.)}, volume = {}, number = {}, pages = {}, doi = {10.1002/art.42616}, pmid = {37219936}, issn = {2326-5205}, abstract = {OBJECTIVE: We aimed to decipher the gut microbiome (GM) and serum metabolic characteristic of individuals at high risk for rheumatoid arthritis (RA) and to investigate the causative effect of GM on the mucosal immune system and its involvement in the pathogenesis of arthritis.<br><br>DESIGN: Fecal samples were collected from 38 healthy individuals (HCs) and 53 high-risk RA individuals with anti-citrullinated protein antibody (ACPA)-positivity (PreRA), 12 of 53 PreRA developed RA within 5&#x2009;years of follow-up. The differences in intestinal microbial composition between the HC and PreRA individuals or among PreRA subgroups were identified by 16S rRNA sequencing. The serum metabolite profile and its correlation with GM were also explored. Moreover, antibiotic-pretreated mice received GM from the HC or PreRA groups were then evaluated for intestinal permeability, inflammatory cytokines and immune cell populations. Collagen-induced arthritis (CIA) was also applied to test the effect of fecal microbiota transplantation (FMT) from PreRA individuals on arthritis severity in mice.<br><br>RESULTS: Stool microbial diversity was lower in PreRA individuals than in HCs. The bacterial community structure and function significantly differed between HC and PreRA individuals. Although there were to some extent differences in the bacterial abundance among the PreRA subgroups, no robust functional differences were observed. The metabolites in the serum of the PreRA group were dramatically different from those in the HC group, with KEGG pathway enrichment of amino acid and lipid metabolism. Moreover, intestinal bacteria from the PreRA group increased intestinal permeability in FMT mice and ZO-1 expression in the small intestine and Caco-2 cells. Moreover, Th17 cells in the mesenteric lymph nodes and Peyer's patches were also increased in mice receiving PreRA feces compared to HC. The changes in intestinal permeability and Th17-cell activation prior to arthritis induction enhanced CIA severity in PreRA-FMT mice compared with HC-FMT mice.<br><br>CONCLUSION: Gut microbial dysbiosis and metabolome alterations already occur in individuals at high risk for RA. FMT from preclinical individuals triggers intestinal barrier dysfunction and changes mucosal immunity, further contributing to arthritis development.}, }
@article {pmid37219498, year = {2023}, author = {Blanco-Míguez, A and Marcos-Fernández, R and Guadamuro-García, L and Fdez-Riverola, F and Cubiella, J and Lourenço, A and Margolles, A and Sánchez, B}, title = {Targeted depletion of pks+ bacteria from a fecal microbiota using specific antibodies.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0007923}, doi = {10.1128/msystems.00079-23}, pmid = {37219498}, issn = {2379-5077}, abstract = {The pks island is one of the most prevalent pathogenicity islands among the Escherichia coli strains that colonize the colon of colorectal carcinoma (CRC) patients. This pathogenic island encodes the production of a nonribosomal polyketide-peptide named colibactin, which induces double-strand breaks in DNA molecules. Detection or even depletion of this pks-producing bacteria could help to understand the role of these strains in the context of CRC. In this work, we performed a large-scale in silico screening of the pks cluster in more than 6,000 isolates of E. coli. The results obtained reveal that not all the pks-detected strains could produce a functional genotoxin and, using antibodies against pks-specific peptides from surface cell proteins, a methodology for detection and depletion of pks+ bacteria in gut microbiotas was proposed. With our method, we were able to deplete a human gut microbiota of this pks+ strains, opening the door to strain-directed microbiota modification and intervention studies that allow us to understand the relation between these genotoxic strains and some gastrointestinal diseases.IMPORTANCEThe human gut microbiome has also been hypothesized to play a crucial role in the development and progression of colorectal carcinoma (CRC). Between the microorganisms of this community, the Escherichia coli strains carrying the pks genomic island were shown to be capable of promoting colon tumorigenesis in a colorectal cancer mouse model, and their presence seems to be directly related to a distinct mutational signature in patients suffering CRC. This work proposes a novel method for the detection and depletion of pks-carrying bacteria in human gut microbiotas. In contrast to methods based on probes, this methodology allows the depletion of low-abundance bacterial strains maintaining the viability of both targeted and non-targeted fractions of the microbiota, allowing the study of the contribution of these pks-carrying strains to different diseases, such as CRC, and their role in other physiological, metabolic or immune processes.}, }
@article {pmid37219436, year = {2023}, author = {Ye, R and Tomo, C and Chan, N and Wolfe, BE}, title = {Penicillium molds impact the transcriptome and evolution of the cheese bacterium Staphylococcus equorum.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0004723}, doi = {10.1128/msphere.00047-23}, pmid = {37219436}, issn = {2379-5042}, abstract = {The observation that Penicillium molds can inhibit the growth of Staphylococcus was a catalyst for the antibiotic revolution. Considerable attention has been paid to purified Penicillium metabolites that inhibit bacteria, but little is known about how Penicillium species impact the ecology and evolution of bacteria in multispecies microbial communities. Here, we investigated how four different species of Penicillium can impact global transcription and evolution of a widespread Staphylococcus species (S. equorum) using the cheese rind model microbiome. Through RNA sequencing, we identified a core transcriptional response of S. equorum against all five tested Penicillium strains, including upregulation of thiamine biosynthesis, fatty acid degradation, and amino acid metabolism as well as downregulation of genes involved in the transport of siderophores. In a 12-week evolution experiment where we co-cultured S. equorum with the same Penicillium strains, we observed surprisingly few non-synonymous mutations across S. equorum populations evolved with the Penicillium species. A mutation in a putative DHH family phosphoesterase gene only occurred in populations evolved without Penicillium and decreased the fitness of S. equorum when co-cultured with an antagonistic Penicillium strain. Our results highlight the potential for conserved mechanisms of Staphylococcus-Penicillium interactions and demonstrate how fungal biotic environments may constrain the evolution of bacterial species.IMPORTANCEFungi and bacteria are commonly found co-occurring both in natural and synthetic microbiomes, but our understanding of fungal-bacterial interactions is limited to a handful of species. Conserved mechanisms of interactions and evolutionary consequences of fungal-bacterial interactions are largely unknown. Our RNA sequencing and experimental evolution data with Penicillium species and the bacterium S. equorum demonstrate that divergent fungal species can elicit conserved transcriptional and genomic responses in co-occurring bacteria. Penicillium molds are integral to the discovery of novel antibiotics and production of certain foods. By understanding how Penicillium species affect bacteria, our work can further efforts to design and manage Penicillium-dominated microbial communities in industry and food production.}, }
@article {pmid37219087, year = {2023}, author = {Gao, Y and Li, D and Liu, YX}, title = {Microbiome research outlook: past, present, and future.}, journal = {Protein &amp; cell}, volume = {}, number = {}, pages = {}, doi = {10.1093/procel/pwad031}, pmid = {37219087}, issn = {1674-8018}, abstract = {With its critical role in human health and disease, the microbiome has transformed modern biology. Over the past few years, microbiome research has evolved rapidly, with microbiologists gradually shifting their focus from cataloging microorganisms in the human microbiome to understanding their functional roles and how they interact with the host. Here, we present the global trends in microbiome research and summarize the past and current work on microbiome published in Protein &amp; Cell. In closing, we highlight some of the major advancements in microbiome research, including technical, practical, and conceptual advancements, that aim to enhance disease diagnosis, medicine development, and personalized interventions.}, }
@article {pmid37218869, year = {2023}, author = {Kurtović, A and Talapko, J and Bekić, S and Škrlec, I}, title = {The Relationship between Sleep, Chronotype, and Dental Caries-A Narrative Review.}, journal = {Clocks &amp; sleep}, volume = {5}, number = {2}, pages = {295-312}, doi = {10.3390/clockssleep5020023}, pmid = {37218869}, issn = {2624-5175}, abstract = {This article provides an overview of how sleep and circadian rhythm disturbances mutually influence the occurrence of dental caries and how it is possible to reduce the risk of circadian rhythm disturbances, sleep, and associated adverse effects. Dental caries is a global problem worldwide that contributes to sociological limitations. Numerous factors influence the occurrence of dental caries, from socioeconomic factors to cariogenic bacteria, dietary habits, and oral hygiene. However, sleep disorders and circadian rhythm disturbances represent a new approach in the fight against the increasing prevalence of dental caries worldwide. Bacteria in the oral cavity and the oral microbiome are mainly responsible for the development of caries, and saliva plays an important role in their regulation. The circadian rhythm regulates numerous physiological functions, including sleep and saliva production. Disturbances in sleep and circadian rhythms affect saliva production, which impacts the development of dental caries, as saliva is necessary for regulating and maintaining oral health, especially for controlling oral infections. A person's preference for a particular time of day depends on the circadian rhythm called chronotype. Individuals with an evening chronotype have a less healthy lifestyle that can lead to a higher caries risk than individuals with a morning chronotype. Because circadian rhythms are critical to maintaining sleep homeostasis and oral health, sleep disturbances can disrupt circadian rhythms and lead to a vicious cycle.}, }
@article {pmid37218816, year = {2023}, author = {Merrick, B and Sergaki, C and Edwards, L and Moyes, DL and Kertanegara, M and Prossomariti, D and Shawcross, DL and Goldenberg, SD}, title = {Modulation of the Gut Microbiota to Control Antimicrobial Resistance (AMR)-A Narrative Review with a Focus on Faecal Microbiota Transplantation (FMT).}, journal = {Infectious disease reports}, volume = {15}, number = {3}, pages = {238-254}, doi = {10.3390/idr15030025}, pmid = {37218816}, issn = {2036-7430}, abstract = {Antimicrobial resistance (AMR) is one of the greatest challenges facing humanity, causing a substantial burden to the global healthcare system. AMR in Gram-negative organisms is particularly concerning due to a dramatic rise in infections caused by extended-spectrum beta-lactamase and carbapenemase-producing Enterobacterales (ESBL and CPE). These pathogens have limited treatment options and are associated with poor clinical outcomes, including high mortality rates. The microbiota of the gastrointestinal tract acts as a major reservoir of antibiotic resistance genes (the resistome), and the environment facilitates intra and inter-species transfer of mobile genetic elements carrying these resistance genes. As colonisation often precedes infection, strategies to manipulate the resistome to limit endogenous infections with AMR organisms, as well as prevent transmission to others, is a worthwhile pursuit. This narrative review presents existing evidence on how manipulation of the gut microbiota can be exploited to therapeutically restore colonisation resistance using a number of methods, including diet, probiotics, bacteriophages and faecal microbiota transplantation (FMT).}, }
@article {pmid37218690, year = {2023}, author = {Murphy, KM and Le, SM and Wilson, AE and Warner, DA}, title = {The Microbiome as A Maternal Effect: A Systematic Review on Vertical Transmission of Microbiota.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icad031}, pmid = {37218690}, issn = {1557-7023}, abstract = {The microbiome is an interactive and fluctuating community of microbes that colonize and develop across surfaces, including those associated with organismal hosts. A growing number of studies exploring how microbiomes vary in ecologically relevant contexts have recognized the importance of microbiomes in affecting organismal evolution. Thus, identifying the source and mechanism for microbial colonization in a host will provide insight into adaptation and other evolutionary processes. Vertical transmission of microbiota is hypothesized to be a source of variation in offspring phenotypes with important ecological and evolutionary implications. However, the life-history traits that govern vertical transmission are largely unexplored in the ecological literature. To increase research attention to this knowledge gap, we conducted a systematic review to address the following questions: 1) How often is vertical transmission assessed as a contributor to offspring microbiome colonization and development? 2) Do studies have the capacity to address how maternal transmission of microbes affects the offspring phenotype? 3) How do studies vary based on taxonomy and life history of the study organism, as well as the experimental, molecular, and statistical methods employed? Extensive literature searches reveal that many studies examining vertical transmission of microbiomes fail to collect whole microbiome samples from both maternal and offspring sources, particularly for oviparous vertebrates. Additionally, studies should sample functional diversity of microbes to provide a better understanding of mechanisms that influence host phenotypes rather than solely taxonomic variation. An ideal microbiome study incorporates host factors, microbe-microbe interactions, and environmental factors. As evolutionary biologists continue to merge microbiome science and ecology, examining vertical transmission of microbes across taxa can provide inferences on causal links between microbiome variation and phenotypic evolution.}, }
@article {pmid37218407, year = {2023}, author = {Renardy, M and Prokopienko, AJ and Maxwell, JR and Flusberg, DA and Makaryan, S and Selimkhanov, J and Vakilynejad, M and Subramanian, K and Wille, L}, title = {A quantitative systems pharmacology model describing the cellular kinetic-pharmacodynamic relationship for a live biotherapeutic product to support microbiome drug development.}, journal = {Clinical pharmacology and therapeutics}, volume = {}, number = {}, pages = {}, doi = {10.1002/cpt.2952}, pmid = {37218407}, issn = {1532-6535}, abstract = {Live biotherapeutic products (LBPs) are human microbiome therapies showing promise in the clinic for a range of diseases and conditions. Describing the kinetics and behavior of LBPs poses a unique modeling challenge since, unlike traditional therapies, LBPs can expand, contract, and colonize the host digestive tract. Here, we present a novel cellular kinetic-pharmacodynamic quantitative systems pharmacology (QSP) model of an LBP. The model describes bacterial growth and competition, vancomycin effects, binding and unbinding to the epithelial surface, and production and clearance of butyrate as a therapeutic metabolite. The model is calibrated and validated to published data from healthy volunteers. Using the model, we simulate the impact of treatment dose, frequency, and duration as well as vancomycin pretreatment on butyrate production. This model enables model-informed drug development (MIDD) and can be used for future microbiome therapies to inform decision making around antibiotic pretreatment, dose selection, loading dose and dosing duration.}, }
@article {pmid37217991, year = {2023}, author = {Meng, Y and Qiu, X and Tang, Z and Mao, Y and Tan, Y}, title = {Lactobacillus paracasei L9 affects disease progression in experimental autoimmune neuritis by regulating intestinal flora structure and arginine metabolism.}, journal = {Journal of neuroinflammation}, volume = {20}, number = {1}, pages = {122}, pmid = {37217991}, issn = {1742-2094}, abstract = {BACKGROUND: Autoimmune neuropathies are common peripheral nervous system (PNS) disorders. Environmental influences and dietary components are known to affect the course of autoimmune diseases. Intestinal microorganisms can be dynamically regulated through diet, and this study combines intestinal microorganisms with diseases to open up new therapeutic ideas.<br><br>METHODS: In Lewis rats, a model of EAN was established with P0 peptide, Lactobacillus were used as treatment, serum T-cell ratio, inflammatory factors, sciatic neuropathological changes, and pathological inflammatory effects on intestinal mucosa were detected, and fecal metabolomics and 16&#xa0;s microbiome analysis were performed to further explore the mechanism.<br><br>RESULTS: In the EAN rat model, Lactobacillus paracasei L9 (LP) could dynamically regulate the CD4[+]/CD8[+]T balance in serum, reduce serum IL-1, IL-6 and TNF-&#x3b1; expression levels, improve sciatic nerve demyelination and inflammatory infiltration, and reduce nervous system score. In the rat model of EAN, intestinal mucosa was damaged. Occludin and ZO-1 were downregulated. IL-1, TNF-&#x3b1; and Reg3&#x3b3; were upregulated. LP gavage induced intestinal mucosa recovery; occludin and ZO-1 upregulation; IL-1, TNF-&#x3b1; and Reg3&#x3b3; downregulation. Finally, metabolomics and 16&#xa0;s microbiome analysis were performed, and differential metabolites were enriched with an important metabolic pathway, arginine and proline metabolism.<br><br>CONCLUSION: LP improved EAN in rats by influencing intestinal community and the lysine and proline metabolism.}, }
@article {pmid37217852, year = {2023}, author = {Scott, DAV and Benavente, E and Libiseller-Egger, J and Fedorov, D and Phelan, J and Ilina, E and Tikhonova, P and Kudryavstev, A and Galeeva, J and Clark, T and Lewin, A}, title = {Bayesian compositional regression with microbiome features via variational inference.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {210}, pmid = {37217852}, issn = {1471-2105}, support = {MR/N013638/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {The microbiome plays a key role in the health of the human body. Interest often lies in finding features of the microbiome, alongside other covariates, which are associated with a phenotype of interest. One important property of microbiome data, which is often overlooked, is its compositionality as it can only provide information about the relative abundance of its constituting components. Typically, these proportions vary by several orders of magnitude in datasets of high dimensions. To address these challenges we develop a Bayesian hierarchical linear log-contrast model which is estimated by mean field Monte-Carlo co-ordinate ascent variational inference (CAVI-MC) and easily scales to high dimensional data. We use novel priors which account for the large differences in scale and constrained parameter space associated with the compositional covariates. A reversible jump Monte Carlo Markov chain guided by the data through univariate approximations of the variational posterior probability of inclusion, with proposal parameters informed by approximating variational densities via auxiliary parameters, is used to estimate intractable marginal expectations. We demonstrate that our proposed Bayesian method performs favourably against existing frequentist state of the art compositional data analysis methods. We then apply the CAVI-MC to the analysis of real data exploring the relationship of the gut microbiome to body mass index.}, }
@article {pmid37217829, year = {2023}, author = {Merenstein, C and Fitzgerald, AS and Khatib, LA and Graham-Wooten, J and Bushman, FD and Collman, RG}, title = {Effects of Mask Reuse on the Oropharyngeal, Skin and Mask Microbiome.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiad167}, pmid = {37217829}, issn = {1537-6613}, abstract = {BACKGROUND: Face masks have been critical in the COVID-19 pandemic, but supplies were sometimes limited and disposable masks contribute greatly to environmental waste. Studies suggest that filtration capacity is retained with repeated use, and surveys indicate many people re-use surgical masks. However, the impact of mask re-use on the host is under-studied.<br><br>METHODS: We applied 16S rRNA gene sequencing to investigate the bacterial microbiome of the facial skin and oropharynx of individuals randomized to wearing fresh surgical masks daily versus masks re-used for one week.<br><br>RESULTS: Compared to daily fresh masks, re-use was associated with increased richness (number of taxa) of the skin microbiome and trend towards greater diversity, but no difference in the oropharyngeal microbiome. Used masks had either skin-dominant or oropharynx-dominant bacterial sequences, and re-used masks had >100-fold higher bacterial content but no change in composition compared to those used for one day.<br><br>CONCLUSIONS: One week of mask re-use increased the number of low-abundance taxa on the face but did not impact the upper respiratory microbiome. Thus, face mask re-use has little impact on the host microbiome, though whether minor changes to the skin microbiome might relate to reported skin sequelae of masking ("maskne") remains to be determined.}, }
@article {pmid37217817, year = {2023}, author = {Srivastava, A and Verma, D}, title = {Urbanization led to the abundance of Gram-negative, chemo-organo-heterotrophs, and antibiotic resistance genes in the downstream regions of the Ganga River water of India.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {37217817}, issn = {1614-7499}, abstract = {The present investigation assesses the bacterial microbiome and antibiotic resistance genes (ARGs) of the river Ganga from Uttarakhand (upstream region; US group) and Uttar Pradesh (downstream region; DS group) regions using a 16S rRNA amplicon-based metagenomic approach. Gram-negative, aerobic, and chemo-organotrophic bacteria made up the majority of the bacterial genera during the overall analysis. Physicochemical analysis revealed a higher concentration of nitrate and phosphate in the downstream sites of the Ganga River. The prevalence of Gemmatimonas, Flavobacterium, Arenimonas, and Verrucomicrobia in the water of the DS region indicates a high organic load. Pseudomonas and Flavobacterium emerged as the most prevalent genera among the 35 significantly different shared genera (p-value < 0.05) in the US and DS regions, respectively. Overall antibiotic resistance analysis of the samples showed the dominance of β-lactam resistance (33.92%) followed by CAMP (cationic antimicrobial peptide) resistance (27.75%), and multidrug resistance (19.17%), vancomycin resistance (17.84%), and tetracycline resistance (0.77%). While comparing, the DS group exhibited a higher abundance of ARGs over the US group, where the CAMP resistance and β-lactam ARGs were dominant in the respective regions. The correlation (p-value < 0.05) analysis showed that most bacteria exhibit a significant correlation with tetracycline resistance followed by the phenicol antibiotic. The present findings draw attention to the need for regulated disposal of multiform human-derived wastes into the Ganga River to reduce the irrepressible ARGs dissemination.}, }
@article {pmid37217624, year = {2023}, author = {Lee, D and Jang, G and Min, KC and Lee, IH and Won, H and Yoon, IJ and Kang, SC and Lee, C}, title = {Coinfection with porcine epidemic diarrhea virus and Clostridium perfringens type A enhances disease severity in weaned pigs.}, journal = {Archives of virology}, volume = {168}, number = {6}, pages = {166}, pmid = {37217624}, issn = {1432-8798}, abstract = {Clostridium perfringens is a constituent of the normal gut microbiome in pigs; however, it can potentially cause pre- and post-weaning diarrhea. Nevertheless, the importance of this bacterium as a primary pathogen of diarrhea in piglets needs to be better understood, and the epidemiology of C. perfringens in Korean pig populations is unknown. To study the prevalence and typing of C. perfringens, 203 fecal samples were collected from diarrheal piglets on 61 swine farms during 2021-2022 and examined for the presence of C. perfringens and enteric viruses, including porcine epidemic diarrhea virus (PEDV). We determined that the most frequently identified type of C. perfringens was C. perfringens type A (CPA; 64/203, 31.5%). Among the CPA infections, single infections with CPA (30/64, 46.9%) and coinfections with CPA and PEDV (29/64, 45.3%) were the most common in diarrheal samples. Furthermore, we conducted animal experiments to investigate the clinical outcome of single infections and coinfections with highly pathogenic (HP)-PEDV and CPA in weaned piglets. The pigs infected with HP-PEDV or CPA alone showed mild or no diarrhea, and none of them died. However, animals that were co-inoculated with HP-PEDV and CPA showed more-severe diarrheal signs than those of the singly infected pigs. Additionally, CPA promoted PEDV replication in coinfected piglets, with high viral titers in the feces. A histopathological examination revealed more-severe villous atrophy in the small intestine of coinfected pigs than in singly infected pigs. This indicates a synergistic effect of PEDV and CPA coinfection on clinical disease in weaned piglets.}, }
@article {pmid37217447, year = {2023}, author = {Weiss, SJ and Hamidi, M}, title = {Maternal stress during the third trimester of pregnancy and the neonatal microbiome.}, journal = {The journal of maternal-fetal &amp; neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians}, volume = {36}, number = {1}, pages = {2214835}, doi = {10.1080/14767058.2023.2214835}, pmid = {37217447}, issn = {1476-4954}, abstract = {OBJECTIVES: Preliminary research suggests that maternal prenatal stress may alter the development of the fetal microbiome and resulting microbial composition after birth. However, the findings of existing studies are mixed and inconclusive. The purpose of this exploratory study was to assess whether maternal stress during pregnancy is associated with the overall number and diversity of various microbial species in the infant gut microbiome or the abundance of specific bacterial taxa.<br><br>METHODS: Fifty-one women were recruited during their third trimester of pregnancy. The women completed a demographic questionnaire and Cohen's Perceived Stress Scale at recruitment. A stool sample was collected from their neonate at one month of age. Data on potential confounders, such as gestational age and mode of delivery, were extracted from medical records to control for their effects. 16s rRNA gene sequencing was used to identify the diversity and abundance of microbial species, along with multiple linear regression models to examine the effects of prenatal stress on microbial diversity. We employed negative binomial generalized linear models to test for differential expression of various microbial taxa among infants exposed to prenatal stress and those not exposed to prenatal stress.<br><br>RESULTS: More severe symptoms of prenatal stress were associated with a greater diversity of microbial species in the gut microbiome of neonates (&#x3b2; = .30, p = .025). Certain microbial taxa, such as Lactobacillus and Bifidobacterium, were enriched among infants exposed to greater maternal stress in utero, while others, such as Bacteroides and Enterobacteriaceae, were depleted in contrast to infants exposed to less stress.<br><br>CONCLUSIONS: Findings suggest that mild to moderate stress exposure in utero could be associated with a microbial environment in early life that is more optimally prepared to thrive in a stressful postnatal environment. Adaptation of gut microbiota under conditions of stress may involve upregulation of bacterial species, including certain protective microorganisms (e.g. Bifidobacterium), as well as downregulation of potential pathogens (e.g. Bacteroides) via epigenetic or other processes within the fetal/neonatal gut-brain axis. However, further research is needed to understand the trajectory of microbial diversity and composition as infant development proceeds and the ways in which both the structure and function of the neonatal microbiome may mediate the relationship between prenatal stress and health outcomes over time. These studies may eventually yield microbial markers and gene pathways that are biosignatures of risk or resilience and inform targets for probiotics or other therapies in utero or during the postnatal period.}, }
@article {pmid37217368, year = {2023}, author = {Aizpurua, O and Blijleven, K and Trivedi, U and Gilbert, MTP and Alberdi, A}, title = {Unravelling animal-microbiota evolution on a chip.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2023.04.010}, pmid = {37217368}, issn = {1878-4380}, abstract = {Whether and how microorganisms have shaped the evolution of their animal hosts is a major question in biology. Although many animal evolutionary processes appear to correlate with changes in their associated microbial communities, the mechanistic processes leading to these patterns and their causal relationships are still far from being resolved. Gut-on-a-chip models provide an innovative approach that expands beyond the potential of conventional microbiome profiling to study how different animals sense and react to microbes by comparing responses of animal intestinal tissue models to different microbial stimuli. This complementary knowledge can contribute to our understanding of how host genetic features facilitate or prevent different microbiomes from being assembled, and in doing so elucidate the role of host-microbiota interactions in animal evolution.}, }
@article {pmid37217284, year = {2023}, author = {Vötterl, JC and Lerch, F and Schwartz-Zimmermann, HE and Sassu, EL and Schwarz, L and Renzhammer, R and Bünger, M and Koger, S and Sharma, S and Sener-Aydemir, A and Quijada, NM and Selberherr, E and Berthiller, F and Metzler-Zebeli, BU}, title = {Plant-oriented microbiome inoculum modulates age-related maturation of gut-mucosal expression of innate immune and barrier function genes in suckling and weaned piglets.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skad165}, pmid = {37217284}, issn = {1525-3163}, abstract = {In the immediate time after weaning, piglets often show symptoms of gut inflammation. The change to a plant-based diet, lack of sow milk and the resulting novel gut microbiome and metabolite profile in digesta may be causative factors for the observed inflammation. We used the intestinal loop perfusion assay (ILPA) to investigate jejunal and colonic expression of genes for antimicrobial secretion, oxidative stress, barrier function and inflammatory signaling in suckling and weaned piglets when exposed to 'plant-oriented' microbiome (POM) representing postweaning digesta with gut-site specific microbial and metabolite composition. Two serial ILPA were performed in two replicate batches, with 16 piglets pre- (day 24-27) and 16 piglets postweaning (day 38-41). Two jejunal and colonic loops were perfused with Krebs-Henseleit buffer (control) or with the respective POM for two hours. Afterwards, RNA was isolated from the loop tissue to determine the relative gene expression. Age-related effects in jejunum included higher expression of genes for antimicrobial secretions and barrier function as well as reduced expression of pattern-recognition receptors post- compared to preweaning (P < 0.05). Age-related effects in the colon comprised downregulation of the expression of pattern-recognition receptors post- compared to preweaning (P < 0.05). Likewise, age reduced the colonic expression of genes encoding for cytokines, antimicrobial secretions, antioxidant enzymes and tight-junction proteins post- compared to preweaning. Effect of POM in the jejunum comprised an increased the expression of toll-like receptors compared to the control (P < 0.05), demonstrating a specific response to microbial antigens. Similarly, POM administration upregulated the jejunal expression of antioxidant enzymes (P < 0.05). The POM perfusion strongly upregulated the colonic expression of cytokines and altered the expression of barrier function genes, fatty acid receptors and transporters and antimicrobial secretions (P < 0.05). In conclusion, results indicated that POM signaled via altering the expression of pattern recognition receptors in the jejunum, which in turn activated the secretory defense and decreased mucosal permeability. In the colon, POM may have acted proinflammatory via upregulated cytokine expression. Results are valuable for the formulation of transition feeds for the immediate time after weaning to maintain mucosal immune tolerance towards the novel digesta composition.}, }
@article {pmid37217203, year = {2023}, author = {Dundore-Arias, JP and Michalska-Smith, M and Millican, M and Kinkel, LL}, title = {More Than the Sum of Its Parts: Unlocking the Power of Network Structure for Understanding Organization and Function in Microbiomes.}, journal = {Annual review of phytopathology}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-phyto-021021-041457}, pmid = {37217203}, issn = {1545-2107}, abstract = {Plant and soil microbiomes are integral to the health and productivity of plants and ecosystems, yet researchers struggle to identify microbiome characteristics important for providing beneficial outcomes. Network analysis offers a shift in analytical framework beyond "who is present" to the organization or patterns of coexistence between microbes within the microbiome. Because microbial phenotypes are often significantly impacted by coexisting populations, patterns of coexistence within microbiomes are likely to be especially important in predicting functional outcomes. Here, we provide an overview of the how and why of network analysis in microbiome research, highlighting the ways in which network analyses have provided novel insights into microbiome organization and functional capacities, the diverse network roles of different microbial populations, and the eco-evolutionary dynamics of plant and soil microbiomes. Expected final online publication date for the Annual Review of Phytopathology, Volume 61 is September 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, }
@article {pmid37217131, year = {2023}, author = {Li, R and Ren, C and Wu, L and Zhang, X and Mao, X and Fan, Z and Cui, W and Zhang, W and Wei, G and Shu, D}, title = {Fertilizing-induced alterations of microbial functional profiles in soil nitrogen cycling closely associate with crop yield.}, journal = {Environmental research}, volume = {}, number = {}, pages = {116194}, doi = {10.1016/j.envres.2023.116194}, pmid = {37217131}, issn = {1096-0953}, abstract = {Fertilization and rhizosphere selection are key regulators for soil nitrogen (N) cycling and microbiome. Thus, clarifying how the overall N cycling processes and soil microbiome respond to these factors is a prerequisite for understanding the consequences of high inputs of fertilizers, enhancing crop yields, and formulating reasonable nitrogen management strategies under agricultural intensification scenarios. To do this, we applied shotgun metagenomics sequencing to reconstruct N cycling pathways on the basis of abundance and distribution of related gene families, as well as explored the microbial diversity and interaction via high throughput sequencing based on a two-decade fertilization experiment in Loess Plateau of China semiarid area. We found that bacteria and fungi respond divergent to fertilization regimes and rhizosphere selection, in terms of community diversity, niche breadth, and microbial co-occurrence networks. Moreover, organic fertilization decreased the complexity of bacterial networks but increased the complexity and stability of fungal networks. Most importantly, rhizosphere selection exerted more strongly influences on the soil overall nitrogen cycling than the application of fertilizers, accompanied by the increase in the abundance of nifH, NIT-6, and narI genes and the decrease in the abundance of amoC, norC, and gdhA genes in the rhizosphere soil. Furthermore, keystone families screening from soil microbiome (e.g., Sphingomonadaceae, Sporichthyaceae, and Mortierellaceae), which were affected by the edaphic variables, contributed greatly to crop yield. Collectively, our findings emphasize the pivotal roles of rhizosphere selection interacting with fertilization regimes in sustaining soil nitrogen cycling processes in response to decades-long fertilization, as well as the potential importance of keystone taxa in maintaining crop yield. These findings significantly facilitate our understanding of nitrogen cycling in diverse agricultural soils and lay a foundation for manipulating specific microorganisms to regulate N cycling and promote agroecosystem sustainability.}, }
@article {pmid37216923, year = {2023}, author = {Ma, Y and Liu, L and Ma, Y and Zhang, S}, title = {HONMF: integration analysis of multi-omics microbiome data via matrix factorization and hypergraph.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btad335}, pmid = {37216923}, issn = {1367-4811}, abstract = {MOTIVATION: The accumulation of multi-omics microbiome data provides an unprecedented opportunity to understand the diversity of bacterial, fungal and viral components from different conditions. The changes in the composition of viruses, bacteria and fungi communities have been associated with environments and critical illness. However, identifying and dissecting the heterogeneity of microbial samples and cross-kingdom interactions remains challenging.<br><br>RESULTS: We propose HONMF for the integrative analysis of multi-modal microbiome data, including bacterial, fungal and viral composition profiles. HONMF enables identification of microbial samples and data visualization, and also facilitates downstream analysis, including feature selection and cross-kingdom association analysis between species. HONMF is an unsupervised method based on hypergraph induced orthogonal nonnegative matrix factorization, where it assumes that latent variables are specific for each composition profile and integrates the distinct sets of latent variables through graph fusion strategy, which better tackles the distinct characteristics in bacterial, fungal and viral microbiome. We implemented HONMF on several multi-omics microbiome datasets from different environments and tissues. The experimental results demonstrate the superior performance of HONMF in data visualization and clustering. HONMF also provides rich biological insights by implementing discriminative microbial feature selection and bacterium-fungus-virus association analysis, which improves our understanding of ecological interactions and microbial pathogenesis.<br><br>AVAILABILITY: The software and datasets are available at https://github.com/chonghua-1983/HONMF.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid37216885, year = {2023}, author = {Guo, W and Zhou, J and Liu, Y and Bai, J and Zhu, Y and Yang, X and Yang, X}, title = {Embryonic injection of Lactobacillus plantarum PA01 alters the microbial diversity in the gastrointestinal tract of the broilers before and after hatching.}, journal = {Poultry science}, volume = {102}, number = {7}, pages = {102764}, doi = {10.1016/j.psj.2023.102764}, pmid = {37216885}, issn = {1525-3171}, abstract = {The total number of intestinal microbiotas is low, and the intestinal tract develops rapidly and imperfectly at the embryonic stage. Embryonic period as a particular physiological stage is an important time window to explore how to regulate organismal health by probiotics. Therefore, this experiment was conducted to investigate the effect of embryonic injection of Lactobacillus plantarum PA01 at embryonic d 14 (E14) on the microbiome of the contents of the gizzard, cecum at embryonic d 20 (E20) and cecum at d 1 posthatch (D1) by 16S rRNA sequencing. Results showed that PA01 had no significant effect on broiler body weight and yolk sac weight at E20 and D1 (P > 0.05). PA-01 altered the Shannon index and β diversity of the gizzard at E20 (P < 0.05), increased the abundance of Firmicutes (P < 0.05), and decreased the relative abundance of Proteobacteria, Bacteroidota, and Actinobacteriota (P < 0.05). At the genus level of the microbiota, PA01 significantly increased the relative abundance of Lactiplantibacillus (P < 0.05). At 20 embryos, PA01 altered the α and β diversity indices (P < 0.05) and decreased the relative abundance of Salmonella (P < 0.05) of the cecal microbiota. The biomarkers of PA01 group were Lactobacillales, Blautia, Lachnospiraceae, and Asinibacterium. Embryonic injection of PA01 altered the E20 intestinal microbes. PA01 altered the β-diversity index of the 1-day-old cecum (P < 0.05), and there was no significant effect on microbial composition at the phylum and genus level (P > 0.05). LefSe analysis revealed that the biomarkers of the PA01 group were Lactobacillaceae, Lactiplantibacillus, Moraxellaceae, and Acinetobacter. Biomarkers in the Con group were Devosia, Bacillus, Nordella, Mesorhizobium, and Pseudolabrys. PA01 increased acetic acid in the gastrointestinal tract at E20 along with acetic and butyric acid in cecum of 1-day-old. In conclusion, embryo-injected L. plantarum PA01 altered the structure and metabolites of the microbial flora before and after hatching, in particular promoting the colonization of Lactobacillus.}, }
@article {pmid37216727, year = {2023}, author = {Fujimoto, D and Shinohara, M and Kawamori, H and Toba, T and Kakizaki, S and Nakamura, K and Sasaki, S and Hamana, T and Fujii, H and Osumi, Y and Hayasaka, N and Kishino, S and Ogawa, J and Hirata, KI and Otake, H}, title = {The relationship between unique gut microbiome-derived lipid metabolites and subsequent revascularization in patients who underwent percutaneous coronary intervention.}, journal = {Atherosclerosis}, volume = {375}, number = {}, pages = {1-8}, doi = {10.1016/j.atherosclerosis.2023.05.001}, pmid = {37216727}, issn = {1879-1484}, abstract = {BACKGROUND AND AIMS: Studies have recently revealed the linoleic acid metabolic pathway of Lactobacillus plantarum, the representative gut bacterium in human gastrointestinal tract, and the anti-inflammatory effects of metabolites in this pathway. However, no clinical trials have evaluated the association between these metabolites and revascularization in patients who underwent percutaneous coronary intervention (PCI).<br><br>METHODS: We retrospectively reviewed patients who underwent PCI with subsequent revascularization or coronary angiography (CAG) without revascularization. Patients with frozen blood samples at the index PCI and revascularization or follow-up CAG were enrolled.<br><br>RESULTS: Among 701 consecutive patients who underwent PCI, we enrolled 53 patients who underwent subsequent revascularization and 161 patients who underwent follow-up CAG without revascularization. Patients who underwent revascularization showed significantly lower plasma 10-oxo-octadecanoic acid (KetoB) levels (720.5 [551.6-876.5] vs. 818.4 [641.1-1103.6 pg/mL]; p&#xa0;=&#xa0;0.01) at index PCI. Multivariate logistic regression analysis revealed that decreased plasma KetoB levels at the index PCI were independently associated with subsequent revascularization after PCI (odds ratio; 0.90 per 100 pg/mL increase, 95% confidence interval; 0.82-0.98). Additionally, in vitro experiments showed that the addition of purified KetoB suppressed the mRNA levels of IL-6 and IL-1&#x3b2; in macrophages and IL-1&#x3b2; mRNA in neutrophils.<br><br>CONCLUSIONS: Plasma KetoB level at index PCI was independently associated with subsequent revascularization after PCI, and KetoB could act as an anti-inflammatory lipid mediator in macrophages and neutrophils. The assessment of gut microbiome-derived metabolites may help predict revascularization after PCI.}, }
@article {pmid37216595, year = {2023}, author = {Zhou, F and Yu, X and Gan, R and Ren, K and Chen, C and Ren, C and Cui, M and Liu, Y and Gao, Y and Wang, S and Yin, M and Huang, T and Huang, Z and Zhang, F}, title = {CRISPRimmunity: an interactive web server for CRISPR-associated Important Molecular events and Modulators Used in geNome edIting Tool identifYing.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkad425}, pmid = {37216595}, issn = {1362-4962}, abstract = {The CRISPR-Cas system is a highly adaptive and RNA-guided immune system found in bacteria and archaea, which has applications as a genome editing tool and is a valuable system for studying the co-evolutionary dynamics of bacteriophage interactions. Here introduces CRISPRimmunity, a new web server designed for Acr prediction, identification of novel class 2 CRISPR-Cas loci, and dissection of key CRISPR-associated molecular events. CRISPRimmunity is built on a suite of CRISPR-oriented databases providing a comprehensive co-evolutionary perspective of the CRISPR-Cas and anti-CRISPR systems. The platform achieved a high prediction accuracy of 0.997 for Acr prediction when tested on a dataset of 99 experimentally validated Acrs and 676 non-Acrs, outperforming other existing prediction tools. Some of the newly identified class 2 CRISPR-Cas loci using CRISPRimmunity have been experimentally validated for cleavage activity in vitro. CRISPRimmunity offers the catalogues of pre-identified CRISPR systems to browse and query, the collected resources or databases to download, a well-designed graphical interface, a detailed tutorial, multi-faceted information, and exportable results in machine-readable formats, making it easy to use and facilitating future experimental design and further data mining. The platform is available at http://www.microbiome-bigdata.com/CRISPRimmunity. Moreover, the source code for batch analysis are published on Github (https://github.com/HIT-ImmunologyLab/CRISPRimmunity).}, }
@article {pmid37216558, year = {2023}, author = {Ghosh, S and Ahearn, CP and Isabella, CR and Marando, VM and Dodge, GJ and Bartlett, H and McPherson, RL and Dugan, AE and Jain, S and Neznanova, L and Tettelin, H and Putnik, R and Grimes, CL and Ruhl, S and Kiessling, LL and Imperiali, B}, title = {Human oral lectin ZG16B acts as a cell wall polysaccharide probe to decode host-microbe interactions with oral commensals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {22}, pages = {e2216304120}, doi = {10.1073/pnas.2216304120}, pmid = {37216558}, issn = {1091-6490}, abstract = {The oral microbiome is critical to human health and disease, yet the role that host salivary proteins play in maintaining oral health is unclear. A highly expressed gene in human salivary glands encodes the lectin zymogen granule protein 16 homolog B (ZG16B). Despite the abundance of this protein, its interaction partners in the oral microbiome are unknown. ZG16B possesses a lectin fold, but whether it binds carbohydrates is unclear. We postulated that ZG16B would bind microbial glycans to mediate recognition of oral microbes. To this end, we developed a microbial glycan analysis probe (mGAP) strategy based on conjugating the recombinant protein to fluorescent or biotin reporter functionality. Applying the ZG16B-mGAP to dental plaque isolates revealed that ZG16B predominantly binds to a limited set of oral microbes, including Streptococcus mitis, Gemella haemolysans, and, most prominently, Streptococcus vestibularis. S. vestibularis is a commensal bacterium widely distributed in healthy individuals. ZG16B binds to S. vestibularis through the cell wall polysaccharides attached to the peptidoglycan, indicating that the protein is a lectin. ZG16B slows the growth of S. vestibularis with no cytotoxicity, suggesting that it regulates S. vestibularis abundance. The mGAP probes also revealed that ZG16B interacts with the salivary mucin MUC7. Analysis of S. vestibularis and MUC7 with ZG16B using super-resolution microscopy supports ternary complex formation that can promote microbe clustering. Together, our data suggest that ZG16B influences the compositional balance of the oral microbiome by capturing commensal microbes and regulating their growth using a mucin-assisted clearance mechanism.}, }
@article {pmid37216534, year = {2023}, author = {Barbour, A and Smith, L and Oveisi, M and Williams, M and Huang, RC and Marks, C and Fine, N and Sun, C and Younesi, F and Zargaran, S and Orugunty, R and Horvath, TD and Haidacher, SJ and Haag, AM and Sabharwal, A and Hinz, B and Glogauer, M}, title = {Discovery of phosphorylated lantibiotics with proimmune activity that regulate the oral microbiome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {22}, pages = {e2219392120}, doi = {10.1073/pnas.2219392120}, pmid = {37216534}, issn = {1091-6490}, abstract = {Lantibiotics are ribosomally synthesized and posttranslationally modified peptides (RiPPs) that are produced by bacteria. Interest in this group of natural products is increasing rapidly as alternatives to conventional antibiotics. Some human microbiome-derived commensals produce lantibiotics to impair pathogens' colonization and promote healthy microbiomes. Streptococcus salivarius is one of the first commensal microbes to colonize the human oral cavity and gastrointestinal tract, and its biosynthesis of RiPPs, called salivaricins, has been shown to inhibit the growth of oral pathogens. Herein, we report on a phosphorylated class of three related RiPPs, collectively referred to as salivaricin 10, that exhibit proimmune activity and targeted antimicrobial properties against known oral pathogens and multispecies biofilms. Strikingly, the immunomodulatory activities observed include upregulation of neutrophil-mediated phagocytosis, promotion of antiinflammatory M2 macrophage polarization, and stimulation of neutrophil chemotaxis-these activities have been attributed to the phosphorylation site identified on the N-terminal region of the peptides. Salivaricin 10 peptides were determined to be produced by S. salivarius strains found in healthy human subjects, and their dual bactericidal/antibiofilm and immunoregulatory activity may provide new means to effectively target infectious pathogens while maintaining important oral microbiota.}, }
@article {pmid37216289, year = {2023}, author = {Groenewegen, B and Terveer, EM and Joosse, A and Barnhoorn, MC and Zwittink, RD}, title = {Fecal Microbiota Transplantation for Immune Checkpoint Inhibitor-Induced Colitis Is Safe and Contributes to Recovery: Two Case Reports.}, journal = {Journal of immunotherapy (Hagerstown, Md. : 1997)}, volume = {}, number = {}, pages = {}, doi = {10.1097/CJI.0000000000000474}, pmid = {37216289}, issn = {1537-4513}, abstract = {Immune checkpoint inhibitors (ICIs) have improved the prognosis in multiple cancer types. However, ICIs can induce immune-related adverse events such as immune-mediated enterocolitis (IMC). The gut microbiota may be implicated in IMC development. Therefore, we investigated fecal microbiota transplantation (FMT) as a treatment option for 2 patients with metastatic cancer suffering from refractory IMC. The patients were treated with, respectively, 1 and 3 FMTs after vancomycin pre-treatment. We monitored defecation frequency, fecal calprotectin, and microbiota composition. After FMT, both patients improved in defecation frequency, were discharged from the hospital, and received lower dosage of immunosuppressive therapy. Patient 1 developed an invasive pulmonary aspergillosis deemed to be related to prolonged steroid exposure. Patient 2 suffered from a Campylobacter jejuni infection after the first FMT and was treated with meropenem, resulting in a low-diversity microbiota profile and increased calprotectin levels and defecation frequency. After a second and third FMT, bacterial diversity increased and defecation frequency and calprotectin levels decreased. Pre-FMT, both patients showed low bacterial richness, but varying bacterial diversity. After FMT, diversity and richness were similar to healthy donor levels. In conclusion, FMT resulted in improvement of IMC symptoms and corresponding microbial changes in 2 cancer patients with refractory IMC. While more research is warranted, microbiome-modulation could be a promising new therapeutic option for IMC.}, }
@article {pmid37216124, year = {2023}, author = {Markandey, M and Bajaj, A and Verma, M and Virmani, S and Singh, MK and Gaur, P and Das, P and Srikanth, CV and Makharia, G and Kedia, S and Ahuja, V}, title = {Fecal microbiota transplantation refurbishes the crypt-associated microbiota in ulcerative colitis.}, journal = {iScience}, volume = {26}, number = {5}, pages = {106738}, doi = {10.1016/j.isci.2023.106738}, pmid = {37216124}, issn = {2589-0042}, abstract = {A crypt autochthonous microbial population called crypt-associated microbiota (CAM) is localized intimately with gut regenerative and immune machinery. The present report utilizes laser capture microdissection coupled with 16S amplicon sequencing to characterize the CAM in patients with ulcerative colitis (UC) before and after fecal microbiota transplantation with anti-inflammatory diet (FMT-AID). Compositional differences in CAM and its interactions with mucosa-associated microbiota (MAM) were compared between the non-IBD controls and in patients with UC pre- and post-FMT (n = 26). Distinct from the MAM, CAM is dominated by aerobic members of Actinobacteria and Proteobacteria and exhibits resilience of diversity. CAM underwent UC-associated dysbiosis and demonstrated restoration post-FMT-AID. These FMT-restored CAM taxa correlated negatively with disease activity in patients with UC. The positive effects of FMT-AID extended further in refurbishing CAM-MAM interactions, which were obliterated in UC. These results encourage investigation into host-microbiome interactions established by CAM, to understand their role in disease pathophysiology.}, }
@article {pmid37215996, year = {2023}, author = {Wang, J and Zhou, T and Liu, F and Huang, Y and Xiao, Z and Qian, Y and Zhou, W}, title = {Influence of gut microbiota on resilience and its possible mechanisms.}, journal = {International journal of biological sciences}, volume = {19}, number = {8}, pages = {2588-2598}, doi = {10.7150/ijbs.82362}, pmid = {37215996}, issn = {1449-2288}, abstract = {Excessive stress leads to disruptions of the central nervous system. Individuals' responses to stress and trauma differ from person to person. Some may develop various neuropsychiatric disorders, such as post-traumatic stress disorder, major depression, and anxiety disorders, while others may successfully adapt to the same stressful events. These two neural phenotypes are called susceptibility and resilience. Previous studies have suggested resilience/susceptibility as a complex, non-specific systemic response involving central and peripheral systems. Emerging research of mechanisms underlying resilience is mostly focussing on the physiological adaptation of specific brain circuits, neurovascular impairment of the blood-brain barrier, the role of innate and adaptive factors of the immune system, and the dysbiosis of gut microbiota. In accordance with the microbiota-gut-brain axis hypothesis, the gut microbiome directly influences the interface between the brain and the periphery to affect neuronal function. This review explored several up-to-date studies on the role of gut microbiota implicated in stressful events-related resilience/susceptibility. We mainly focus on the changes in behavior and neuroimaging characteristics, involved brain regions and circuits, the blood-brain barrier, the immune system, and epigenetic modifications, which contribute to stress-induced resilience and susceptibility. The perspective of the gut-brain axis could help to understand the mechanisms underlying resilience and the discovery of biomarkers may lead to new research directions and therapeutic interventions for stress-induced neuropsychiatric disorders.}, }
@article {pmid37215555, year = {2023}, author = {Shen, Y and Wang, P and Yang, X and Chen, M and Dong, Y and Li, J}, title = {A cross-sectional study identifying disparities in serum metabolic profiles among hypertensive patients with ISH, IDH and SDH subtypes.}, journal = {Frontiers in cardiovascular medicine}, volume = {10}, number = {}, pages = {1102754}, doi = {10.3389/fcvm.2023.1102754}, pmid = {37215555}, issn = {2297-055X}, abstract = {BACKGROUND: It has been well acknowledged that disordered intestinal microflora and their fermented products play crucial role during the development of hypertension (HTN). Aberrant profiles of fecal bacteria have been documented in subjects with isolated systolic HTN (ISH) and isolated diastolic HTN (IDH) previously. Nevertheless, evidence regarding the association of metabolic products in the bloodstream with ISH, IDH and combined systolic and diastolic HTN (SDH) remains scarce.<br><br>METHODS: We performed a cross-sectional study and conducted untargeted liquid chromatography-mass spectrometry (LC/MS) analysis on serum samples of 119 participants, including 13 subjects with normotension (SBP&#x2009;<&#x2009;120/DBP&#x2009;<&#x2009;80&#x2005;mm Hg), 11 individuals with ISH (SBP&#x2009;&#x2265;&#x2009;130/DBP&#x2009;<&#x2009;80&#x2005;mm Hg), 27 patients with IDH (SBP&#x2009;<&#x2009;130/DBP&#x2009;&#x2265;&#x2009;80&#x2005;mm Hg), and 68 SDH patients (SBP&#x2009;&#x2265;&#x2009;130, DBP&#x2009;&#x2265;&#x2009;80&#x2005;mm Hg).<br><br>RESULTS: Here, the results showed clearly separated clusters in PLS-DA and OPLS-DA score plots for patients suffering from ISH, IDH and SDH when compared with normotension controls. The ISH group was characterized by elevated levels of 3,5-tetradecadien carnitine and notable reduction of maleic acid. While IDH patients were enriched with metabolites in L-lactic acid and depleted in citric acid. Stearoylcarnitine was identified to be specifically enriched in SDH group. The differentially abundant metabolites between ISH and controls were involved in tyrosine metabolism pathways, and in biosynthesis of phenylalanine for those between SDH and controls. Potential linkages between the gut microbial and serum metabolic signatures were detected within ISH, IDH and SDH groups. Furthermore, we found the association of discriminatory metabolites with the characteristics of patients.<br><br>CONCLUSION: Our findings demonstrate disparate blood metabolomics signatures across ISH, IDH and SDH, with differentially enriched metabolites and potential functional pathways identified, reveal the underlying microbiome and metabolome network in HTN subtypes, and provide potential targets for disease classification and therapeutic strategy in clinical practice.}, }
@article {pmid37215554, year = {2023}, author = {Li, Y and Fu, R and Li, R and Zeng, J and Liu, T and Li, X and Jiang, W}, title = {Causality of gut microbiome and hypertension: A bidirectional mendelian randomization study.}, journal = {Frontiers in cardiovascular medicine}, volume = {10}, number = {}, pages = {1167346}, doi = {10.3389/fcvm.2023.1167346}, pmid = {37215554}, issn = {2297-055X}, abstract = {BACKGROUND &amp; AIMS: The pathogenesis of hypertension involves a diverse range of genetic, environmental, hemodynamic, and more causative factors. Recent evidence points to an association between the gut microbiome and hypertension. Given that the microbiota is in part determined by host genetics, we used the two-sample Mendelian randomization (MR) analysis to address the bidirectional causal link between gut microbiota and hypertension.<br><br>METHODS: We selected genetic variants (P&#x2009;<&#x2009;1&#x2009;&#x2009;&#xd7;&#x2009;&#x2009;10[-5]) for gut microbiota (n&#x2009;=&#x2009;18,340) from the MiBioGen study. Genetic association estimates for hypertension were extracted from genome-wide association study (GWAS) summary statistics on 54,358 cases and 408,652 controls. Seven complementary MR methods were implemented, including the inverse-variance weighted (IVW) method, followed by sensitivity analyses to verify the robustness of the results. Reverse-direction MR analyses were further conducted to probe if there was a reverse causative relationship. Bidirectional MR analysis then examines a modulation of gut microbiota composition by hypertension.<br><br>RESULTS: At the genus level, our MR estimates from gut microbiome to hypertension showed that there were 5 protective factors Allisonella, Parabacteroide, Phascolarctobacterium, Senegalimassilia, and unknowngenus (id.1000000073), while 6 genera Clostridiuminnocuum, Eubacteriumcoprostanoligenes, Eubacteriumfissicatena, Anaerostipes, LachnospiraceaeFCS020, and unknowngenus (id.2041) are risk factors. The Alcaligenaceae and ClostridialesvadinBB60 were detrimental and beneficial at the family level, respectively. In contrast, the MR results of hypertension-gut flora showed hypertensive states can lead to an increased abundance of Eubacteriumxylanophilum, Eisenbergiella, and Lachnospiraceae and a lower abundance of Alistipes, Bilophila, Butyricimonas, and Phascolarctobacterium.<br><br>CONCLUSION: Altered gut microbiota is a causal factor in the development of hypertension, and hypertension causes imbalances in the intestinal flora. Substantial research is still needed to find the key gut flora and explore the specific mechanisms of their effects so that new biomarkers can be found for blood pressure control.}, }
@article {pmid37215258, year = {2023}, author = {Yeo, J}, title = {Influence of food-derived bioactives on gut microbiota compositions and their metabolites by focusing on neurotransmitters.}, journal = {Food science and biotechnology}, volume = {32}, number = {8}, pages = {1019-1027}, doi = {10.1007/s10068-023-01293-2}, pmid = {37215258}, issn = {2092-6456}, abstract = {The behavior of gut microbiota is closely involved in sustaining balanced immune and metabolic homeostasis, and the dysbiosis of gut microbiota can lead to severe disease. Foods and dietary patterns are the primary drivers in shaping/designing gut microbiota compositions and their metabolites across the lifetime. This indicates the importance of functional molecules present in the food matrix in the life of gut microbiota and their influence on the host's biological system. In this contribution, the effects of different dietary choices and bioactive compounds (i.e., phenolics, vitamins, carotenoids) on gut microbiome compositions and their metabolites are comprehensively discussed by focusing on neurotransmitters. This study may provide useful information that fills a gap in understanding the role of the gut microbiota and its alterations as affected by foods and food-derived bioactives.}, }
@article {pmid37215132, year = {2023}, author = {Zhang, L and Wang, F and Jia, L and Yan, H and Gao, L and Tian, Y and Su, X and Zhang, X and Lv, C and Ma, Z and Xue, Y and Lin, Q and Wang, K}, title = {Edwardsiella piscicida infection reshapes the intestinal microbiome and metabolome of big-belly seahorses: mechanistic insights of synergistic actions of virulence factors.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1135588}, doi = {10.3389/fimmu.2023.1135588}, pmid = {37215132}, issn = {1664-3224}, abstract = {Uncovering the mechanism underlying the pathogenesis of Edwardsiella piscicida-induced enteritis is essential for global aquaculture. In the present study, we identified E. piscicida as a lethal pathogen of the big-belly seahorse (Hippocampus abdominalis) and revealed its pathogenic pattern and characteristics by updating our established bacterial enteritis model and evaluation system. Conjoint analysis of metagenomic and metabolomic data showed that 15 core virulence factors could mutually coordinate the remodeling of intestinal microorganisms and host metabolism and induce enteritis in the big-belly seahorse. Specifically, the Flagella, Type IV pili, and Lap could significantly increase the activities of the representative functional pathways of both flagella assembly and bacterial chemotaxis in the intestinal microbiota (P < 0.01) to promote pathogen motility, adherence, and invasion. Legiobactin, IraAB, and Hpt could increase ABC transporter activity (P < 0.01) to compete for host nutrition and promote self-replication. Capsule1, HP-NAP, and FarAB could help the pathogen to avoid phagocytosis. Upon entering epithelial cells and phagocytes, Bsa T3SS and Dot/Icm could significantly increase bacterial secretion system activity (P < 0.01) to promote the intracellular survival and replication of the pathogen and the subsequent invasion of the neighboring tissues. Finally, LPS3 could significantly increase lipopolysaccharide biosynthesis (P < 0.01) to release toxins and kill the host. Throughout the pathogenic process, BopD, PhoP, and BfmRS significantly activated the two-component system (P < 0.01) to coordinate with other VFs to promote deep invasion. In addition, the levels of seven key metabolic biomarkers, Taurine, L-Proline, Uridine, L-Glutamate, Glutathione, Xanthosine, and L-Malic acid, significantly decreased (P < 0.01), and they can be used for characterizing E. piscicida infection. Overall, the present study systematically revealed how a combination of virulence factors mediate E. piscicida-induced enteritis in fish for the first time, providing a theoretical reference for preventing and controlling this disease in the aquaculture of seahorses and other fishes.}, }
@article {pmid37215122, year = {2023}, author = {Homan, EJ and Bremel, RD}, title = {Determinants of tumor immune evasion: the role of T cell exposed motif frequency and mutant amino acid exposure.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1155679}, doi = {10.3389/fimmu.2023.1155679}, pmid = {37215122}, issn = {1664-3224}, abstract = {Few neoepitopes detected in tumor biopsies are immunogenic. Tumor-specific T cell responses require both the presentation of an epitope that differs from wildtype and the presence of T cells with neoepitope-cognate receptors. We show that mutations detected in tumor biopsies result in an increased frequency of rare amino acid combinations compared to the human proteome and gastrointestinal microorganisms. Mutations in a large data set of oncogene and tumor suppressor gene products were compared to wildtype, and to the count of corresponding amino acid motifs in the human proteome and gastrointestinal microbiome. Mutant amino acids in T cell exposed positions of potential neoepitopes consistently generated amino acid motifs that are less common in both proteome reference datasets. Approximately 10% of the mutant amino acid motifs are absent from the human proteome. Motif frequency does not change when mutants were positioned in the MHC anchor positions hidden from T cell receptors. Analysis of neoepitopes in GBM and LUSC cases showed less common T cell exposed motifs, and HLA binding preferentially placing mutant amino acids in an anchor position for both MHC I and MHC II. Cross-presentation of mutant exposed neoepitopes by MHC I and MHC II was particularly uncommon. Review of a tumor mutation dataset known to generate T cell responses showed immunogenic epitopes were those with mutant amino acids exposed to the T cell receptor and with exposed pentamer motifs present in the human and microbiome reference databases. The study illustrates a previously unrecognized mechanism of tumor immune evasion, as rare T cell exposed motifs produced by mutation are less likely to have cognate T cells in the T cell repertoire. The complex interactions of HLA genotype, binding positions, and mutation specific changes in T cell exposed motif underscore the necessity of evaluating potential neoepitopes in each individual patient.}, }
@article {pmid37215102, year = {2023}, author = {Young, KZ and Dimitrion, P and Zhou, L and Adrianto, I and Mi, QS}, title = {Sex-biased immunological processes drive hidradenitis suppurativa.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1167021}, doi = {10.3389/fimmu.2023.1167021}, pmid = {37215102}, issn = {1664-3224}, abstract = {Hidradenitis suppurativa (HS) is a chronic inflammatory skin condition that can manifest with abscesses, sinus tracts, and scarring in the intertriginous areas of the body. HS is characterized by immune dysregulation, featuring elevated levels of myeloid cells, T helper (Th) cells, and pro-inflammatory cytokines, particularly those involved in Th1- and Th17-mediated immunity. In most epidemiological studies, HS shows a strong female sex bias, with reported female-to-male ratios estimated at roughly 3:1, suggesting that sex-related factors contribute to HS pathophysiology. In this article, we review the role of intrinsic and extrinsic factors that contribute to immunological differences between the sexes and postulate their role in the female sex bias observed in HS. We discuss the effects of hormones, X chromosome dosage, genetics, the microbiome, and smoking on sex-related differences in immunity to postulate potential immunological mechanisms in HS pathophysiology. Future studies are required to better characterize sex-biased factors that contribute to HS disease presentations.}, }
@article {pmid37215085, year = {2023}, author = {Li, YJ and Ma, J and Loh, YW and Chadban, SJ and Wu, H}, title = {Short-chain fatty acids directly exert anti-inflammatory responses in podocytes and tubular epithelial cells exposed to high glucose.}, journal = {Frontiers in cell and developmental biology}, volume = {11}, number = {}, pages = {1182570}, doi = {10.3389/fcell.2023.1182570}, pmid = {37215085}, issn = {2296-634X}, abstract = {Aims: Gut-microbiome derived short-chain fatty acids exert anti-inflammatory effects and delay progression of kidney disease in diabetic nephropathy. The aim of this study was to examine the impact in vivo and in vitro of short-chain fatty acid treatment on cellular pathways involved in the development of experimental diabetic nephropathy. Methods: To determine the effect of short-chain fatty acids in diabetic nephropathy, we compared wildtype, GPR43-/- and GPR109A-/- mice diabetic mice treated with acetate or butyrate and assessed variables of kidney damage. We also examined the impact of short-chain fatty acid treatment on gene expression in renal tubular cells and podocytes under high glucose conditions. Results: Short-chain fatty acid treatment with acetate or butyrate protected wild-type mice against development of diabetic nephropathy, exhibiting less glomerular hypertrophy, hypercellularity and interstitial fibrosis compared to diabetic controls. Acetate and butyrate treatment did not provide the same degree of protection in diabetic GPR43-/- and GPR109A-/- diabetic mice respectively. Consistent with our in vivo results, expression of pro-inflammatory genes in tubular epithelial cells exposed to high glucose were attenuated by acetate and butyrate treatment. Acetate did not reduce inflammatory or fibrotic responses in glucose stimulated GPR43-/- TECs. Butyrate mediated inhibition of pro-fibrotic gene expression in TECs through GPR109A, and in podocytes via GPR43. Conclusion: SCFAs protect against progression of diabetic nephropathy and diminish podocyte and tubular epithelial injury and interstitial fibrosis via direct, GPR-pathway dependent effects on intrinsic kidney cells. GPR43 and GPR109A are critical to short-chain fatty acid mediated reno-protection and have potential to be harnessed as a therapeutic target in diabetic nephropathy.}, }
@article {pmid37215025, year = {2023}, author = {Trinh, P and Roberts, MC and Rabinowitz, PM and Willis, AD}, title = {Differences in gut metagenomes between dairy workers and community controls: a cross-sectional study.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.05.10.540270}, pmid = {37215025}, abstract = {BACKGROUND: As a nexus of routine antibiotic use and zoonotic pathogen presence, the live-stock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens as they undergo evolution prior to a spillover event. In light of this, we are interested in characterizing the microbiome and resistome of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases.<br><br>RESULTS: Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of the human gut microbiome of 10 dairy farm workers and 6 community controls, supplementing these samples with additional publicly available gut metagenomes. We observed greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes in dairy workers' metagenomes, and lower average gene diversity. We also found evidence of commensal organism association with plasmid-mediated tetracycline resistance genes in both dairy workers and community controls (including Faecalibacterium prausnitzii, Ligilactobacillus animalis , and Simiaoa sunii). However, we did not find significant differences in the prevalence of resistance genes or virulence factors overall, nor differences in the taxonomic composition of dairy worker and community control metagenomes.<br><br>CONCLUSIONS: This study presents the first metagenomics analysis of United States dairy workers, providing insights into potential risks of exposure to antibiotics and pathogens in animal farming environments. Previous metagenomic studies of livestock workers in China and Europe have reported increased abundance and carriage of antibiotic resistance genes in livestock workers. While our investigation found no strong evidence for differences in the abundance or carriage of antibiotic resistance genes and virulence factors between dairy worker and community control gut metagenomes, we did observe patterns in the abundance of tetracycline resistance genes and the prevalence of cephamycin resistance genes that is consistent with previous work.}, }
@article {pmid37215022, year = {2023}, author = {Accoti, A and Multini, LC and Diouf, B and Becker, M and Vulcan, J and Sylla, M and Yap, DAY and Khanipov, K and Weaver, SC and Diallo, M and Gaye, A and Dickson, LB}, title = {The influence of the larval microbiome on susceptibility to Zika virus is mosquito genotype dependent.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.05.10.540191}, pmid = {37215022}, abstract = {The microbiome of the mosquito Aedes aegypti is largely determined by the environment and influences mosquito susceptibility for arthropod-borne viruses (arboviruses). Larval interactions with different bacteria can influence adult Ae. aegypti replication of arboviruses, but little is known about the role that mosquito host genetics play in determining how larval-bacterial interactions shape Ae aegypti susceptibility to arboviruses. To address this question, we isolated single bacterial isolates and complex microbiomes from Ae. aegypti larvae from various field sites in Senegal. Either single bacterial isolates or complex microbiomes were added to two different genetic backgrounds of Ae. aegypti in a gnotobiotic larval system. Using 16S amplicon sequencing we show that similarities in bacterial community structures when given identical microbiomes between different genetic backgrounds of Ae. aegypti was dependent on the source microbiome, and the abundance of single bacterial taxa differed between Ae. aegypti genotypes. Using single bacterial isolates or the entire preserved complex microbiome, we tested the ability of specific microbiomes to drive differences in infection rates for Zika virus in different genetic backgrounds of Ae. aegypti . We observed that the proportion of Zika virus-infected adults was dependent on the interaction between the larval microbiome and Ae. aegypti host genetics. By using the larval microbiome as a component of the environment, these results demonstrate that interactions between the Ae. aegypti genotype and its environment can influence Zika virus infection. As Ae. aegypti expands and adapts to new environments under climate change, an understanding of how different genotypes interact with the same environment will be crucial for implementing arbovirus transmission control strategies.}, }
@article {pmid37214985, year = {2023}, author = {Merchak, AR and Wachamo, S and Brown, LC and Thakur, A and Moreau, B and Brown, RM and Rivet-Noor, C and Raghavan, T and Gaultier, A}, title = {Lactobacillus maintains IFNγ homeostasis to promote behavioral stress resilience.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.05.10.540223}, pmid = {37214985}, abstract = {The gut microbiome consists of the trillions of bacteria, fungi, and viruses that inhabit the digestive tract. These communities are sensitive to disruption from environmental exposures ranging from diet changes to illness. Disruption of the community of lactic acid producing bacteria, Lactobaccillacea , has been well documented in mood disorders and stress exposure. In fact, oral supplement with many Lactobacillus species can ameliorate these effects, preventing depression- and anxiety-like behavior. Here, for the first time, we utilize a gnotobiotic mouse colonized with the Altered Schaedler Flora to remove the two native species of Lactobaccillacea . Using this novel microbial community, we found that the Lactobacillus species themselves, and not the disrupted microbial communities are protective from environmental stressors. Further, we determine that Lactobaccillacea are maintaining homeostatic IFNγ levels which are mediating these behavioral and circuit level responses. By utilizing the Altered Schaedler Flora, we have gained new insight into how probiotics influence behavior and give novel methods to study potential therapies developed to treat mood disorders.}, }
@article {pmid37214959, year = {2023}, author = {Moldovan, OT and Carrell, AA and Bulzu, PA and Levei, E and Bucur, R and Sitar, C and Faur, L and Mirea, IC and Enilă, M and Cadar, O and Podar, M}, title = {The gut microbiome mediates adaptation to scarce food in Coleoptera.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.05.12.540564}, pmid = {37214959}, abstract = {Beetles are ubiquitous cave invertebrates worldwide that adapted to scarce subterranean resources when they colonized caves. Here, we investigated the potential role of gut microbiota in the adaptation of beetles to caves from different climatic regions of the Carpathians. The beetles' microbiota was host-specific, reflecting phylogenetic and nutritional adaptation. The microbial community structure further resolved conspecific beetles by caves suggesting microbiota-host coevolution and influences by local environmental factors. The detritivore species hosted a variety of bacteria known to decompose and ferment organic matter, suggesting turnover and host cooperative digestion of the sedimentary microbiota and allochthonous-derived nutrients. The cave Carabidae, with strong mandibulae adapted to predation and scavenging of animal and plant remains, had distinct microbiota dominated by symbiotic lineages Spiroplasma or Wolbachia . All beetles had relatively high levels of fermentative Carnobacterium and Vagococcus involved in lipid accumulation and a reduction of metabolic activity, and both features characterize adaptation to caves.}, }
@article {pmid37214910, year = {2023}, author = {Moyne, O and Al-Bassam, M and Lieng, C and Thiruppathy, D and Norton, GJ and Kumar, M and Haddad, E and Zaramela, LS and Zengler, K}, title = {Guild and Niche Determination Enable Targeted Alteration of the Microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.05.11.540389}, pmid = {37214910}, abstract = {Microbiome science has greatly contributed to our understanding of microbial life and its essential roles for the environment and human health [1-5] . However, the nature of microbial interactions and how microbial communities respond to perturbations remains poorly understood, resulting in an often descriptive and correlation-based approach to microbiome research [6-8] . Achieving causal and predictive microbiome science would require direct functional measurements in complex communities to better understand the metabolic role of each member and its interactions with others. In this study we present a new approach that integrates transcription and translation measurements to predict competition and substrate preferences within microbial communities, consequently enabling the selective manipulation of the microbiome. By performing metatranscriptomic (metaRNA-Seq) and metatranslatomic (metaRibo-Seq) analysis in complex samples, we classified microbes into functional groups (i.e. guilds) and demonstrated that members of the same guild are competitors. Furthermore, we predicted preferred substrates based on importer proteins, which specifically benefited selected microbes in the community (i.e. their niche) and simultaneously impaired their competitors. We demonstrated the scalability of microbial guild and niche determination to natural samples and its ability to successfully manipulate microorganisms in complex microbiomes. Thus, the approach enhances the design of pre- and probiotic interventions to selectively alter members within microbial communities, advances our understanding of microbial interactions, and paves the way for establishing causality in microbiome science.}, }
@article {pmid37214901, year = {2023}, author = {Eggers, S and Midya, V and Bixby, M and Gennings, C and Torres-Olascoaga, LA and Walker, RW and Wright, RO and Arora, M and Téllez-Rojo, MM}, title = {Prenatal Lead Exposure is Negatively Associated with the Gut Microbiome in Childhood.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.05.10.23289802}, pmid = {37214901}, abstract = {BACKGROUND: Metal exposures are associated with gut microbiome (GM) composition and function, and exposures early in development may be particularly important. Considering the role of the GM in association with many adverse health outcomes, understanding the relationship between prenatal metal exposures and the GM is critically important. However, there is sparse knowledge of the association between prenatal metal exposure and GM later in childhood.<br><br>OBJECTIVES: This analysis aims to identify associations between prenatal lead (Pb) exposure and GM composition and function in children 9-11 years old.<br><br>METHODS: Data come from the Programming Research in Obesity, Growth, Environment and Social Stressors (PROGRESS) cohort based in Mexico City, Mexico. Prenatal metal concentrations were measured in maternal whole blood drawn during the second and third trimesters of pregnancy. Stool samples collected at 9-11 years old underwent metagenomic sequencing to assess the GM. This analysis uses multiple statistical modeling approaches, including linear regression, permutational analysis of variance, weighted quantile sum regression (WQS), and individual taxa regressions, to estimate the association between maternal blood Pb during pregnancy and multiple aspects of the child GM at 9-11 years old, adjusting for relevant confounders.<br><br>RESULTS: Of the 123 child participants in this pilot data analysis, 74 were male and 49 were female. Mean prenatal maternal blood Pb was 33.6(SE=2.1) ug/L and 34.9(SE=2.1) ug/L at second and third trimesters, respectively. Analysis suggests a consistent negative relationship between prenatal maternal blood Pb and the GM at age 9-11, including measures of alpha and beta diversity, microbiome mixture analysis, and individual taxa. The WQS analysis showed a negative association between prenatal Pb exposure and the gut microbiome, for both second and third trimester exposures (2T&#x3b2;=-0.17,95%CI=[-0.46,0.11]; 3T&#x3b2;=-0.17,95%CI=[-0.44,0.10]). Ruminococcus gnavus, Bifidobacterium longum, Alistipes indistinctus, Bacteroides caccae, and Bifidobacterium bifidum all had weights above the importance threshold from 80% or more of the WQS repeated holdouts in association with both second and third trimester Pb exposure.<br><br>DISCUSSION: Pilot data analysis suggests a negative association between prenatal Pb exposure and the gut microbiome later in childhood; however, additional investigation is needed.}, }
@article {pmid37214858, year = {2023}, author = {Bleich, RM and Li, C and Sun, S and Barlogio, CJ and Broberg, CA and Franks, AR and Bulik-Sullivan, E and Dogan, B and Simpson, KW and Carroll, IM and Fodor, AA and Arthur, JC}, title = {A consortia of clinical E. coli strains with distinct in-vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-2899665/v1}, pmid = {37214858}, abstract = {Background Inflammatory bowel disease (IBD) patients experience recurrent episodes of intestinal inflammation and often follow an unpredictable disease course. Mucosal colonization with adherent-invasive Escherichia coli (AIEC) are believed to perpetuate intestinal inflammation. However, it remains unclear if the 24-year-old AIEC in-vitro definition fully predicts mucosal colonization in-vivo . To fill this gap, we have developed a novel molecular barcoding approach to distinguish strain variants in the gut and have integrated this approach to explore mucosal colonization of distinct patient-derived E. coli isolates in gnotobiotic mouse models of colitis. Results Germ-free inflammation-susceptible interleukin-10-deficient (Il10 [-/-]) and inflammation-resistant WT mice were colonized with a consortia of AIEC and non-AIEC strains, then given a murine fecal transplant to provide niche competition. E. coli strains isolated from human intestinal tissue were each marked with a unique molecular barcode that permits identification and quantification by barcode-targeted sequencing. 16S rRNA sequencing was used to evaluate the microbiome response to E. coli colonization. Our data reveal that specific AIEC and non-AIEC strains reproducibly colonize the intestinal mucosa of WT and Il10 [-/-] mice. These E. coli expand in Il10 [-/-] mice during inflammation and induce compositional dysbiosis to the microbiome in an inflammation-dependent manner. In turn, specific microbes co-evolve in inflamed mice, potentially diversifying E. coli colonization patterns. We observed no selectivity in E. coli colonization patterns in the fecal contents, indicating minimal selective pressure in this niche from host-microbe and interbacterial interactions. Because select AIEC and non-AIEC strains colonize the mucosa, this suggests the in vitro AIEC definition may not fully predict in vivo colonization potential. Further comparison of seven E. coli genomes pinpointed unique genomic features contained only in highly colonizing strains (two AIEC and two non-AIEC). Those colonization-associated features may convey metabolic advantages (e.g., iron acquisition and carbohydrate consumption) to promote efficient mucosal colonization. Conclusions Our findings establish the in-vivo mucosal colonizer, not necessarily AIEC, as a principal dysbiosis driver through crosstalk with host and associated microbes. Furthermore, we highlight the utility of high-throughput screens to decode the in-vivo colonization dynamics of patient-derived bacteria in murine models.}, }
@article {pmid37214811, year = {2023}, author = {Rojas, CA and Marks, SL and Borras, E and Lesea, H and McCartney, MM and Coil, D and Davis, CE and Eisen, JA}, title = {Characterization of the microbiome and volatile compounds in anal gland secretions from domestic cats (Felis catus) using metagenomics and metabolomics.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-2883555/v1}, pmid = {37214811}, abstract = {Animals rely on volatile chemical compounds for their communication and behavior. Many of these compounds are sequestered in endocrine and exocrine glands and are synthesized by anaerobic microbes. While the volatile organic compound (VOC) or microbiome composition of glandular secretions has been investigated in several mammalian species, few have linked specific bacterial taxa to the production of volatiles or to specific microbial gene pathways. Here, we use metagenomic sequencing, mass-spectrometry based metabolomics, and culturing to profile the microbial and volatile chemical constituents of anal gland secretions in twenty-three domestic cats (Felis catus), in attempts to identify organisms potentially involved in host odor production. We found that the anal gland microbiome was dominated by bacteria in the genera Corynebacterium , Bacteroides , Proteus , Lactobacillus , and Streptococcus , and showed striking variation among individual cats. Microbiome profiles also varied with host age and obesity. Metabolites such as fatty-acids, ketones, aldehydes and alcohols were detected in glandular secretions. Overall, microbiome and metabolome profiles were modestly correlated (r=0.17), indicating that a relationship exists between the bacteria in the gland and the metabolites produced in the gland. Functional analyses revealed the presence of genes predicted to code for enzymes involved in VOC metabolism such as dehydrogenases, reductases, and decarboxylases. From metagenomic data, we generated 85 high-quality metagenome assembled genomes (MAGs). Of these, four were inferred to have high relative abundance in metagenome profiles and had close relatives that were recovered as cultured isolates. These four MAGs were classified as Corynebacterium frankenforstense , Proteus mirabilis , Lactobacillus johnsonii , and Bacteroides fragilis . They represent strong candidates for further investigation of the mechanisms of volatile synthesis and scent production in the mammalian anal gland.}, }
@article {pmid37214789, year = {2023}, author = {Mendez Luque, LF and Avelar-Barragan, J and Nguyen, H and Nguyen, J and Soyfer, EM and Liu, J and Chen, JH and Mehrotra, N and Kosiorek, HE and Dueck, A and Himstead, A and Heide, E and Lem, M and El Alaoui, K and Mas Marin, E and Scherber, RM and Mesa, RA and Whiteson, KL and Odegaard, A and Fleischman, AG}, title = {The NUTRIENT Trial (NUTRitional Intervention among myEloproliferative Neoplasms): Feasibility Phase.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.05.09.23289740}, pmid = {37214789}, abstract = {PURPOSE: Chronic inflammation is integral to Myeloproliferative Neoplasm (MPN) pathogenesis. JAK inhibitors reduce cytokine levels, but not without significant side effects. Nutrition is a low-risk approach to reduce inflammation and ameliorate symptoms in MPN. We performed a randomized, parallel-arm study to determine the feasibility of an education-focused Mediterranean diet intervention among MPN patients.<br><br>EXPERIMENTAL DESIGN: We randomly assigned participants to either a Mediterranean diet or standard US Dietary Guidelines for Americans (USDA). Groups received equal but separate education with registered dietician counseling and written dietary resources. Patients were prospectively followed for feasibility, adherence, and symptom burden assessments. Biological samples were collected at four time points during the 15-week study to explore changes in inflammatory biomarkers and gut microbiome.<br><br>RESULTS: The Mediterranean diet was as easy to follow for MPN patients as the standard USDA diet. Over 80% of the patients in the Mediterranean diet group achieved a Mediterranean Diet Adherence Score of &#x2265;8 throughout the entire active intervention period, whereas less than 50% of the USDA group achieved a score of &#x2265;8 at any time point. Improvement in symptom burden was observed in both diet groups. No significant changes were observed in inflammatory cytokines. The diversity and composition of the gut microbiome remained stable throughout the duration of the intervention.<br><br>CONCLUSIONS: With dietician counseling and written education MPN patients can adhere to a Mediterranean eating pattern. Diet interventions may be further developed as a component of MPN care, and potentially even be incorporated into the management of other chronic clonal hematologic conditions.<br><br>Chronic clonal hematologic disorders, such as myeloproliferative neoplasm (MPN), lie at the intersection between malignancy and chronic inflammatory disease. Chronic inflammation is responsible for many of the clinical consequences of MPN. Diet is a central tenant of management of chronic conditions characterized by subclinical inflammation, such as cardiovascular disease, but has not entered the treatment algorithm for clonal hematologic disorders. Here, we establish that a Mediterranean diet intervention is feasible in the MPN patient population and can improve symptom burden. These findings warrant large dietary interventions in patients with clonal hematologic disorders to test the utility of diet in improvement of clinical outcomes.}, }
@article {pmid37214608, year = {2023}, author = {Yue, R and Chen, H and Xu, X and Xia, Y and Sun, Y and Xia, M and Xia, D and Sun, B}, title = {Maternal and infantile gut mycobiome during the weaning period in free ranging Tibetan macaques (Macaca thibetana).}, journal = {Ecology and evolution}, volume = {13}, number = {5}, pages = {e10108}, doi = {10.1002/ece3.10108}, pmid = {37214608}, issn = {2045-7758}, abstract = {Gut microbiome is critical to the health of mammals. Many previous studies have revealed the gut bacterial microbiomes of mother and infant changed significantly during the weaning period. However, little is known concerning the gut mycobiome of wild primates. Here, we examined the variations on gut mycobiome between weaning and post-weaning for both mother and infant in wild-living Tibetan macaques (Macaca thibetana). Our results showed that the gut mycobiomes of mother and infant were dominated by two phyla Ascomycota and Basidiomycota. For both mother and infant, the ASV richness of gut mycobiome remained relatively steady from weaning to post-weaning periods, while the Shannon indexes increased significant in weaning compared to post-weaning periods. However, no significant difference between mother and infant ASV richness and Shannon indexes during weaning and post-weaning periods respectively. Compared to mothers, we found that much more known taxa of gut fungi were enriched in weaning or post-weaning periods of infants. In particular, we found that the dominant genus Aspergillus was enriched in infants during weaning period. Furthermore, we found that the relative abundance of plant pathogens were significantly higher in the post-weaning period than in the weaning period for infants. Our results indicated that weaning events could affect the gut mycobiome significantly for both mothers and infant in Tibetan macaques, which had a stronger effect on the gut mycobiome of infant monkeys than on their mothers.}, }
@article {pmid37214349, year = {2023}, author = {Auria, E and Deschamps, J and Briandet, R and Dupuy, B}, title = {Extracellular succinate induces spatially organized biofilm formation in Clostridioides difficile.}, journal = {Biofilm}, volume = {5}, number = {}, pages = {100125}, doi = {10.1016/j.bioflm.2023.100125}, pmid = {37214349}, issn = {2590-2075}, abstract = {Clostridioides difficile infection associated to gut microbiome dysbiosis is the leading cause for nosocomial diarrhea. The ability of C. difficile to form biofilms has been progressively linked to its pathogenesis as well as its persistence in the gut. Although C. difficile has been reported to form biofilms in an increasing number of conditions, little is known about how these biofilms are formed in the gut and what factors may trigger their formation. Here we report that succinate, a metabolite abundantly produced by the dysbiotic gut microbiota, induces in vitro biofilm formation of C. difficile strains. We characterized the morphology and spatial composition of succinate-induced biofilms, and compared to non-induced or deoxycholate (DCA) induced biofilms. Biofilms induced by succinate are significantly thicker, structurally more complex, and poorer in proteins and exopolysaccharides (EPS). We then applied transcriptomics and genetics to characterize the early stages of succinate-induced biofilm formation and we showed that succinate-induced biofilm results from major metabolic shifts and cell-wall composition changes. Similar to DCA-induced biofilms, biofilms induced by succinate depend on the presence of a rapidly metabolized sugar. Finally, although succinate can be consumed by the bacteria, we found that the extracellular succinate is in fact responsible for the induction of biofilm formation through complex regulation involving global metabolic regulators and the osmotic stress response. Thus, our work suggests that as a gut signal, succinate may drive biofilm formation and help persistence of C. difficile in the gut, increasing the risk of relapse.}, }
@article {pmid37214215, year = {2023}, author = {Zhao, Y and Yu, S and Li, L and Zhao, H and Li, Y and Jiang, L and Liu, M}, title = {Feeding citrus flavonoid extracts decreases bacterial endotoxin and systemic inflammation and improves immunometabolic status by modulating hindgut microbiome and metabolome in lactating dairy cows.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {13}, number = {}, pages = {386-400}, doi = {10.1016/j.aninu.2023.03.007}, pmid = {37214215}, issn = {2405-6383}, abstract = {The objectives of this study were to determine the effects of dietary supplementation with citrus flavonoid extracts (CFE) on milk performance, serum biochemistry parameters, fecal volatile fatty acids, fecal microbial community, and fecal metabolites in dairy cows. Eight multiparous lactating Holstein cows were used in a replicated 4 × 4 Latin square design (21-day period). Cows were fed a basal diet without addition (CON) or basal diet with added CFE at 50 (CFE50), 100 (CFE10), and 150 g/d (CFE150). Feeding CFE up to 150 g/d increased milk yield and milk lactose percentage. Supplementary CFE linearly decreased milk somatic cell count. Serum cytokines interleukin-1β (IL-1β), IL-2, IL-6, and tumor necrosis factor-α (TNF-α) concentrations decreased linearly as the levels of CFE increased. Cows in CFE150 had lower serum lipopolysaccharide and lipopolysaccharide binding protein compared with CON. These results indicate feeding CFE decreased systemic inflammation and endotoxin levels in dairy cows. Furthermore, feeding CFE linearly increased the concentrations of total volatile fatty acids, acetate, and butyrate in feces. The relative abundances of beneficial bacteria Bifidobacterium spp., Clostridium coccoides-Eubacterium rectale group, and Faecalibacterium prausnitzii in feces increased linearly with increasing CFE supplementation. The diversity and community structure of fecal microbiota were unaffected by CFE supplementation. However, supplementing CFE reduced the relative abundances of genera Ruminococcus_torques_group, Roseburia, and Lachnospira, but increased genera Bacteroides and Phascolarctobacterium. Metabolomics analysis showed that supplementary CFE resulted in a significant modification in the fecal metabolites profile. Compared with CON, fecal naringenin, hesperetin, hippuric acid, and sphingosine concentrations were greater in CFE150 cows, while fecal GlcCer(d18:1/20:0), Cer(d18:0/24:0), Cer(d18:0/22:0), sphinganine, and deoxycholic acid concentrations were less in CFE150 cows. Predicted pathway analysis suggested that "sphingolipid metabolism" was significantly enriched. Overall, these results indicate that citrus flavonoids could exert health-promoting effects by modulating hindgut microbiome and metabolism in lactating cows.}, }
@article {pmid37214166, year = {2023}, author = {Gestels, T and Vandenplas, Y}, title = {Prenatal and Perinatal Antibiotic Exposure and Long-Term Outcome.}, journal = {Pediatric gastroenterology, hepatology &amp; nutrition}, volume = {26}, number = {3}, pages = {135-145}, doi = {10.5223/pghn.2023.26.3.135}, pmid = {37214166}, issn = {2234-8646}, abstract = {Antibiotics are frequently administered during pregnancy. Although necessary to address acute infections, their use facilitates antibiotic resistance. Other associations have also been found with the use of antibiotics, such as perturbations of gut bacteria, delays in microbial maturation, and increased risks of allergic and inflammatory diseases. Little is known about how the prenatal and perinatal administration of antibiotics to mothers affects the clinical outcomes of their offspring. A literature search was conducted of the Cochrane, Embase, and PubMed engines. The retrieved articles were reviewed by two authors and verified for relevance. The primary outcome was the effect of pre- and perinatal maternal antibiotic use on clinical outcomes. Thirty-one relevant studies were included in the meta-analysis. Various aspects are discussed, including infections, allergies, obesity, and psychosocial factors. In animal studies, antibiotic intake during pregnancy has been suggested to cause long-term alterations in immune regulation. In humans, associations have been found between antibiotic intake during pregnancy and different types of infections and an increased risk of pediatric infection-related hospitalization. A dose-dependent positive association between pre- and perinatal antibiotic use and asthma severity has been reported in animal and human studies, while positive associations with atopic dermatitis and eczema were reported by human studies. Multiple associations were identified between antibiotic intake and psychological problems in animal studies; however, relevant data from human studies are limited. However, one study reported a positive association with autism spectrum disorders. Multiple animal and human studies reported a positive association between pre- and perinatal antibiotic use by mothers and diseases in their offspring. Our findings have potentially significant clinical relevance, particularly considering the implications for health during infancy and later in life as well as the related economic burden.}, }
@article {pmid37213669, year = {2023}, author = {Chao, YT and Lin, YK and Chen, LK and Huang, P and Hsu, YC}, title = {Role of the gut microbiota and their metabolites in hemodialysis patients.}, journal = {International journal of medical sciences}, volume = {20}, number = {6}, pages = {725-736}, pmid = {37213669}, issn = {1449-1907}, abstract = {High serum phosphate levels in chronic kidney disease (CKD) are linked to adverse health outcomes, including cardiovascular disease, kidney disease progression, and all-cause mortality. This study is aimed to find out which microorganisms or microbial functions have a significant impact on higher calcium-phosphorus product (Ca x P) after they undergo hemodialysis (HD) treatment. Feces samples from 30 healthy controls, 15 dialysis patients with controlled Ca xP (HD), and 16 dialysis patients with higher Ca xP (HDHCP) were collected to perform in 16S amplicon sequencing. We found gut microbial composition was significantly different between hemodialysis patients and healthy controls. Three phyla including Firmicutes, Actinobacteria, and Proteobacteria were significantly enriched in hemodialysis patients. Although only one genus, Lachnospiraceae_FCS020_group, was significantly increased in higher Ca xP group, there were four metabolic pathways predicted by PICRUSt significantly increased in higher Ca xP group and associated with causing VC, including the pentose phosphate pathway, steroid biosynthesis, terpenoid backbone biosynthesis, and fatty acid elongation pathway. Characterizing dysbiosis of gut microbiome played the important role in hemodialysis patients.}, }
@article {pmid37213612, year = {2023}, author = {Zdziarski, P and Paściak, M and Chudzik, A and Kozińska, M and Augustynowicz-Kopeć, E and Gamian, A}, title = {Cutaneous tuberculosis-ambiguous transmission, bacterial diversity with biofilm formation in humoral abnormality: case report illustration.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1091373}, pmid = {37213612}, issn = {2296-2565}, abstract = {BACKGROUND: Cutaneous tuberculosis (CTB) and its paucibacillary forms are rare and difficult to diagnose, especially in immunocompromised patients with significant comorbidity. The aim of the study was to introduce the modern concept of the microbiome and diagnostic chain into clinical practice (patient-centered care) with the presentation of an atypical form of cutaneous tuberculosis with necrotizing non-healing ulcers leading to polymicrobial infection.<br><br>METHODS: The study material included samples from sputum, broncho-alveolar lavage and skin ulcer, taken from a patient developing cutaneous tuberculosis. The microbiological investigation was performed, and identification of the isolates was carried out using genotyping and the matrix-assisted laser desorption ionization-time of flight mass spectrometry.<br><br>RESULTS: The immunocompromised patient with humoral abnormality (plasma cell dyscrasia) and severe paraproteinemia developed multiorgan tuberculosis. Although cutaneous manifestation preceded systemic and pulmonary symptoms (approximately half a year), the mycobacterial genotyping confirmed the same MTB strain existence in skin ulcers and the respiratory system. Therefore, the infectious chain: transmission, the portal of entry, and bacterial spreading in vivo, were unclear. Microbial diversity found in wound microbiota (among others Gordonia bronchialis, Corynebacterium tuberculostearicum, Staphylococcus haemolyticus, and Pseudomonas oryzihabitans) was associated with the spread of a skin lesion. The in vitro biofilm-forming capacity of strains isolated from the wound may represent the potential virulence of these strains. Thus, the role of polymicrobial biofilm may be crucial in ulcer formation and CTB manifestation.<br><br>CONCLUSIONS: Severe wound healing as a unique biofilm-forming niche should be tested for Mycobacterium (on species and strain levels) and coexisting microorganisms using a wide range of microbiological techniques. In immunodeficient patients with non-typical CTB presentation, the chain of transmission and MTB spread is still an open issue for further research.}, }
@article {pmid37213556, year = {2023}, author = {Babalola, OO and Olowe, OM and Ayangbenro, AS}, title = {Corrigendum to "Shotgun metagenomics dataset of Striga hermonthica-infested maize (Zea mays L.) rhizospheric soil microbiome" [Data in Brief, volume 48 (2023) 1-5/109132].}, journal = {Data in brief}, volume = {48}, number = {}, pages = {109191}, doi = {10.1016/j.dib.2023.109191}, pmid = {37213556}, issn = {2352-3409}, abstract = {[This corrects the article DOI: 10.1016/j.dib.2023.109132.].}, }
@article {pmid37213524, year = {2023}, author = {Park, I and Seo, YS and Mannaa, M}, title = {Recruitment of the rhizo-microbiome army: assembly determinants and engineering of the rhizosphere microbiome as a key to unlocking plant potential.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1163832}, pmid = {37213524}, issn = {1664-302X}, abstract = {The viable community of microorganisms in the rhizosphere significantly impacts the physiological development and vitality of plants. The assembly and functional capacity of the rhizosphere microbiome are greatly influenced by various factors within the rhizosphere. The primary factors are the host plant genotype, developmental stage and status, soil properties, and resident microbiota. These factors drive the composition, dynamics, and activity of the rhizosphere microbiome. This review addresses the intricate interplay between these factors and how it facilitates the recruitment of specific microbes by the host plant to support plant growth and resilience under stress. This review also explores current methods for engineering and manipulating the rhizosphere microbiome, including host plant-mediated manipulation, soil-related methods, and microbe-mediated methods. Advanced techniques to harness the plant's ability to recruit useful microbes and the promising use of rhizo-microbiome transplantation are highlighted. The goal of this review is to provide valuable insights into the current knowledge, which will facilitate the development of cutting-edge strategies for manipulating the rhizosphere microbiome for enhanced plant growth and stress tolerance. The article also indicates promising avenues for future research in this field.}, }
@article {pmid37213523, year = {2023}, author = {Świątczak, J and Kalwasińska, A and Szabó, A and Swiontek Brzezinska, M}, title = {Pseudomonas sivasensis 2RO45 inoculation alters the taxonomic structure and functioning of the canola rhizosphere microbial community.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1168907}, pmid = {37213523}, issn = {1664-302X}, abstract = {Inoculation with plant growth-promoting rhizobacteria (PGPR) is an eco-friendly sustainable strategy for improving crop productivity in diverse environments under different conditions. Our earlier study demonstrated that Pseudomonas sivasensis 2RO45 significantly stimulated canola (Brassica napus L. var. napus) growth. The aim of the present study was to investigate the structural and functional dynamics in the canola rhizosphere microbiome after inoculation with PGPR P. sivasensis 2RO45. The results based on alpha diversity metrics showed that P. sivasensis 2RO45 did not significantly alter the diversity of the native soil microbiota. However, the introduced strain modified the taxonomic structure of microbial communities, increasing the abundance of plant beneficial microorganisms, e.g., bacteria affiliated with families Comamonadaceae, Vicinamibacteraceae, genus Streptomyces, and fungi assigned to Nectriaceae, Didymellaceae, Exophiala, Cyphellophora vermispora, and Mortierella minutissima. The analysis of community level physiological profiling (CLPP) revealed that microbial communities in the P. sivasensis 2RO45 treated canola rhizospheres were more metabolically active than those in the non-treated canola rhizosphere. Four carbon sources (phenols, polymers, carboxylic acids, and amino acids) were better metabolized by the microbial communities from the rhizosphere of plants inoculated with the P. sivasensis 2RO45 than non-inoculated canola rhizospheres. Based on the community-level physiological profiles, the functional diversity of the rhizosphere microbiome was altered by the P. sivasensis 2RO45 inoculation. Substrate utilization Shannon diversity (H) index and evenness (E) index were significantly increased in the treated canola plants. The study provides new insight into PGPR-canola interactions for sustainable agriculture development.}, }
@article {pmid37213506, year = {2023}, author = {Zhang, Y and Zhang, J and Wu, J and Zhu, Q and Chen, C and Li, Y}, title = {Implications of gut microbiota dysbiosis and fecal metabolite changes in psychologically stressed mice.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1124454}, pmid = {37213506}, issn = {1664-302X}, abstract = {INTRODUCTION: Psychological stress can induce affective disorders. Gut microbiota plays a vital role in emotional function regulation; however, the association between gut microbiota and psychological stress is poorly understood. We investigated effects of psychological stress on the gut microbiome and fecal metabolites and assessed the relationship between affective disorder behavior and altered fecal microbiota.<br><br>METHODS: A psychological stress model was established in C57BL/6J mice using a communication box. Sucrose preference test, forced swim test, and open field test helped assess anxiety- and depression-like behaviors. Fecal microbiota transplantation (FMT) was conducted using fecal samples from stressed and non-stressed mice. Moreover, 16S rRNA gene sequencing and untargeted metabolomics were performed.<br><br>RESULTS: After stress exposure for 14 days, a significant increase in anxiety- and depression-like behaviors was observed. FMT of "affective disorder microbiota" from psychologically stressed mice increased stress sensitivity relative to FMT of "normal microbiota" from non-stressed mice. 16S rRNA gene sequencing revealed decreased abundance of Bacteroides, Alistipes, and Lactobacillus and increased abundance of Parasutterella and Rikenellaceae_RC9_gut_group in stressed mice; furthermore, stressed mice showed differential metabolite profiles. KEGG pathway analysis indicated that differential metabolites were chiefly involved in the downregulated pathways of &#x3b1;-linolenic acid metabolism, taste transduction, and galactose metabolism. Alistipes and Bacteroides were mainly positively correlated and Parasutterella was mainly negatively correlated with diverse metabolites.<br><br>DISCUSSION: Our findings suggest that gut microbiome dysbiosis contributes to affective disorder development in response to psychological stress.}, }
@article {pmid37213502, year = {2023}, author = {Díaz, M and Monfort-Lanzas, P and Quiroz-Moreno, C and Rivadeneira, E and Castillejo, P and Arnau, V and Díaz, W and Agathos, SN and Sangari, FJ and Jarrín-V, P and Molina, CA}, title = {The microbiome of the ice-capped Cayambe Volcanic Complex in Ecuador.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1154815}, pmid = {37213502}, issn = {1664-302X}, abstract = {A major challenge in microbial ecology is to understand the principles and processes by which microbes associate and interact in community assemblages. Microbial communities in mountain glaciers are unique as first colonizers and nutrient enrichment drivers for downstream ecosystems. However, mountain glaciers have been distinctively sensitive to climate perturbations and have suffered a severe retreat over the past 40 years, compelling us to understand glacier ecosystems before their disappearance. This is the first study in an Andean glacier in Ecuador offering insights into the relationship of physicochemical variables and altitude on the diversity and structure of bacterial communities. Our study covered extreme Andean altitudes at the Cayambe Volcanic Complex, from 4,783 to 5,583 masl. Glacier soil and ice samples were used as the source for 16S rRNA gene amplicon libraries. We found (1) effects of altitude on diversity and community structure, (2) the presence of few significantly correlated nutrients to community structure, (3) sharp differences between glacier soil and glacier ice in diversity and community structure, where, as quantified by the Shannon γ-diversity distribution, the meta-community in glacier soil showed more diversity than in glacier ice; this pattern was related to the higher variability of the physicochemical distribution of variables in the former substrate, and (4) significantly abundant genera associated with either high or low altitudes that could serve as biomarkers for studies on climate change. Our results provide the first assessment of these unexplored communities, before their potential disappearance due to glacier retreat and climate change.}, }
@article {pmid37213501, year = {2023}, author = {Huang, Y and Jiang, P and Liang, Z and Chen, R and Yue, Z and Xie, X and Guan, C and Fang, X}, title = {Assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1145315}, pmid = {37213501}, issn = {1664-302X}, abstract = {Human gut microbiota is associated with human health and disease, and is known to have the second-largest genome in the human body. The microbiota genome is important for their functions and metabolites; however, accurate genomic access to the microbiota of the human gut is hindered due to the difficulty of cultivating and the shortcomings of sequencing technology. Therefore, we applied the stLFR library construction method to assemble the microbiota genomes and demonstrated that assembly property outperformed standard metagenome sequencing. Using the assembled genomes as references, SNP, INDEL, and HGT gene analyses were performed. The results demonstrated significant differences in the number of SNPs and INDELs among different individuals. The individual displayed a unique species variation spectrum, and the similarity of strains within individuals decreased over time. In addition, the coverage depth analysis of the stLFR method shows that a sequencing depth of 60X is sufficient for SNP calling. HGT analysis revealed that the genes involved in replication, recombination and repair, mobilome prophages, and transposons were the most transferred genes among different bacterial species in individuals. A preliminary framework for human gut microbiome studies was established using the stLFR library construction method.}, }
@article {pmid37213490, year = {2023}, author = {Jackson, R and Patapiou, PA and Golding, G and Helanterä, H and Economou, CK and Chapuisat, M and Henry, LM}, title = {Evidence of phylosymbiosis in Formica ants.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1044286}, pmid = {37213490}, issn = {1664-302X}, abstract = {INTRODUCTION: Insects share intimate relationships with microbes that play important roles in their biology. Yet our understanding of how host-bound microbial communities assemble and perpetuate over evolutionary time is limited. Ants host a wide range of microbes with diverse functions and are an emerging model for studying the evolution of insect microbiomes. Here, we ask whether phylogenetically related ant species have formed distinct and stable microbiomes.<br><br>METHODS: To answer this question, we investigated the microbial communities associated with queens of 14 Formica species from five clades, using deep coverage 16S rRNA amplicon sequencing.<br><br>RESULTS: We reveal that Formica species and clades harbor highly defined microbial communities that are dominated by four bacteria genera: Wolbachia, Lactobacillus, Liliensternia, and Spiroplasma. Our analysis reveals that the composition of Formica microbiomes mirrors the phylogeny of the host, i.e., phylosymbiosis, in that related hosts harbor more similar microbial communities. In addition, we find there are significant correlations between microbe co-occurrences.<br><br>DISCUSSION: Our results demonstrate Formica ants carry microbial communities that recapitulate the phylogeny of their hosts. Our data suggests that the co-occurrence of different bacteria genera may at least in part be due to synergistic and antagonistic interactions between microbes. Additional factors potentially contributing to the phylosymbiotic signal are discussed, including host phylogenetic relatedness, host-microbe genetic compatibility, modes of transmission, and similarities in host ecologies (e.g., diets). Overall, our results support the growing body of evidence that microbial community composition closely depends on the phylogeny of their hosts, despite bacteria having diverse modes of transmission and localization within the host.}, }
@article {pmid37213286, year = {2023}, author = {Zhen, J and Liu, C and Liao, F and Zhang, J and Xie, H and Tan, C and Dong, W}, title = {The global research of microbiota in colorectal cancer screening: a bibliometric and visualization analysis.}, journal = {Frontiers in oncology}, volume = {13}, number = {}, pages = {1169369}, pmid = {37213286}, issn = {2234-943X}, abstract = {AIMS: We conducted bibliometric and visualization analyses to evaluate the current research status, hotspots, and trends related to the human microbiota markers in colorectal cancer screening.<br><br>METHODS: The related studies were acquired from the Web of Science Core Collection (WoSCC) database on 5 January 2023. Analyses of the co-occurrence and cooperation relationships between the cited authors, institutions, countries/regions, cited journals, cited articles, and keywords in the studies were carried out using CiteSpace 5.8.R3 software and the Online Analysis platform of Literature Metrology. Additionally, relevant knowledge graphs were drawn to perform visualization analyses; a keywords cluster analysis and a burst analysis were also conducted.<br><br>RESULTS: After analyzing 700 relevant articles, this bibliometric analysis found that the annual publications showed an increasing trend from 1992 to 2022. Yu Jun from the Chinese University of Hong Kong had the highest cumulative number of publications, whereas Shanghai Jiao Tong University was the most productive institution. China and the USA have contributed the largest number of studies. The keywords frequency analysis demonstrated that "colorectal cancer," "gut microbiota," "Fusobacterium nucleatum," "risk," and "microbiota" were the most frequent keywords, and the keywords cluster analysis found that the current hotspots were as follows: (a) the precancerous lesions of colorectal cancer (CRC) that need to be screened, such as inflammatory bowel disease (IBD) and advanced adenoma, (b) the gut-derived microbiome for CRC screening, and (c) the early detection of CRC. The burst analysis further showed that the combination of microbiomics with metabolomics might be the future research trend in the field of CRC screening.<br><br>CONCLUSION: The findings of the current bibliometric analysis firstly provide an insight into the current research status, hotspots, and future trends in the field of CRC screening based on the microbiome; the research in this field is becoming more in-depth and diversified. Some human microbiota markers, especially "Fusobacterium nucleatum," are promising biomarkers in CRC screening, and a future hotspot might be the combined analysis of microbiomics and metabolomics for CRC risk screening.}, }
@article {pmid37213223, year = {2023}, author = {Scanes, E and Siboni, N and Rees, B and Seymour, JR}, title = {Acclimation in intertidal animals reduces potential pathogen load and increases survival following a heatwave.}, journal = {iScience}, volume = {26}, number = {6}, pages = {106813}, pmid = {37213223}, issn = {2589-0042}, abstract = {Intertidal animals can experience intense heat during a heatwave, leading to mortality. The causes of death for intertidal animals following heatwaves have often been attributed to a breakdown in physiological processes. This, however, contrasts with research in other animals where heatwave mortality is attributed to existing or opportunistic diseases. We acclimated intertidal oysters to four treatment levels, including an antibiotic treatment, and then exposed all treatments to a 50°C heatwave for 2 h, replicating what can be experienced on Australian shorelines. We found that both acclimation and antibiotics increased survival and reduced the presence of potential pathogens. Non-acclimated oysters had a significant shift in their microbiome, with increasing abundances of bacteria from the Vibrio genera, including known potential pathogens. Our results demonstrate that bacterial infection plays a pivotal role in post-heatwave mortality. We anticipate these findings to inform the management of aquaculture and intertidal habitats as climate change intensifies.}, }
@article {pmid37213060, year = {2023}, author = {Vallianou, NG and Evangelopoulos, A and Kounatidis, D and Panagopoulos, F and Geladari, E and Karampela, I and Stratigou, T and Dalamaga, M}, title = {Immunotherapy in Head and Neck Cancer: Where Do We Stand?.}, journal = {Current oncology reports}, volume = {}, number = {}, pages = {}, pmid = {37213060}, issn = {1534-6269}, abstract = {PURPOSEOF REVIEW: Head and neck cancer (HNC) comprises a group of malignancies, amongst which squamous cell carcinoma accounts for more than 90% of the cases. HNC has been related to tobacco use, alcohol consumption, human papillomavirus, Epstein-Barr virus, air pollution, and previous local radiotherapy. HNC has been associated with substantial morbidity and mortality. This review aims to summarize the recent findings regarding immunotherapy in HNC.<br><br>RECENT FINDINGS: The recent introduction of immunotherapy, with the use of programmed death 1 (PD-1) inhibitors pembrolizumab and nivolumab, which have been FDA approved for the treatment of metastatic or recurrent head and neck squamous cell carcinoma, has changed the field in metastatic or recurrent disease. There are many ongoing trials regarding the use of novel immunotherapeutic agents, such as durvalumab, atezolizumab, avelumab, tremelimumab, and monalizumab. In this review, we focus on the therapeutic potential of novel immunotherapy treatment modalities, such as combinations of newer immune-checkpoint inhibitors; the use of tumor vaccines such as human papillomavirus-targeted vaccines; the potential use of oncolytic viruses; as well as the latest advances regarding adoptive cellular immunotherapy. As novel treatment options are still emerging, a more personalized approach to metastatic or recurrent HNC therapy should be followed. Moreover, the role of the microbiome in immunotherapy, the limitations of immunotherapy, and the various diagnostic, prognostic, and predictive biomarkers based on genetics and the tumor microenvironment are synopsized.}, }
@article {pmid37213047, year = {2023}, author = {Chaudhari, DS and Jain, S and Yata, VK and Mishra, SP and Kumar, A and Fraser, A and Kociolek, J and Dangiolo, M and Smith, A and Golden, A and Masternak, MM and Holland, P and Agronin, M and White-Williams, C and Arikawa, AY and Labyak, CA and Yadav, H}, title = {Unique trans-kingdom microbiome structural and functional signatures predict cognitive decline in older adults.}, journal = {GeroScience}, volume = {}, number = {}, pages = {}, pmid = {37213047}, issn = {2509-2723}, abstract = {The prevalence of age-related cognitive disorders/dementia is increasing, and effective prevention and treatment interventions are lacking due to an incomplete understanding of aging neuropathophysiology. Emerging evidence suggests that abnormalities in gut microbiome are linked with age-related cognitive decline and getting acceptance as one of the pillars of the Geroscience hypothesis. However, the potential clinical importance of gut microbiome abnormalities in predicting the risk of cognitive decline in older adults is unclear. Till now the majority of clinical studies were done using 16S rRNA sequencing which only accounts for analyzing bacterial abundance, while lacking an understanding of other crucial microbial kingdoms, such as viruses, fungi, archaea, and the functional profiling of the microbiome community. Utilizing data and samples of older adults with mild cognitive impairment (MCI; n = 23) and cognitively healthy controls (n = 25). Our whole-genome metagenomic sequencing revealed that the gut of older adults with MCI harbors a less diverse microbiome with a specific increase in total viruses and a decrease in bacterial abundance compared with controls. The virome, bacteriome, and microbial metabolic signatures were significantly distinct in subjects with MCI versus controls. Selected bacteriome signatures show high predictive potential of cognitive dysfunction than virome signatures while combining virome and metabolic signatures with bacteriome boosts the prediction power. Altogether, the results from our pilot study indicate that trans-kingdom microbiome signatures are significantly distinct in MCI gut compared with controls and may have utility for predicting the risk of developing cognitive decline and dementia- debilitating public health problems in older adults.}, }
@article {pmid37212718, year = {2023}, author = {Tian, B and Qu, Z and Mehmood, MA and Xie, J and Cheng, J and Fu, Y and Jiang, D}, title = {Schizotrophic Sclerotinia sclerotiorum-Mediated Root and Rhizosphere Microbiome Alterations Activate Growth and Disease Resistance in Wheat.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0098123}, doi = {10.1128/spectrum.00981-23}, pmid = {37212718}, issn = {2165-0497}, abstract = {Sclerotinia sclerotiorum, a widespread pathogen of dicotyledons, can grow endophytically in wheat, providing protection against Fusarium head blight and stripe rust and enhancing wheat yield. In this study, we found that wheat seed treatment with strain DT-8, infected with S. sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1) and used as a "plant vaccine" for brassica protection, could significantly increase the diversity of the fungal and bacterial community in rhizosphere soil, while the diversity of the fungal community was obviously decreased in the wheat root. Interestingly, the relative abundance of potential plant growth-promoting rhizobacteria (PGPR) and biocontrol agents increased significantly in the DT-8-treated wheat rhizosphere soil. These data might be responsible for wheat growth promotion and disease resistance. These results may provide novel insights for understanding the interaction between the schizotrophic microorganism and the microbiota of plant roots and rhizosphere, screening and utilizing beneficial microorganisms, and further reducing chemical pesticide utilization and increasing crop productivity. IMPORTANCE Fungal pathogens are seriously threatening food security and natural ecosystems; efficient and environmentally friendly control methods are essential to increase world crop production. S. sclerotiorum, a widespread pathogen of dicotyledons, can grow endophytically in wheat, providing protection against Fusarium head blight and stripe rust and enhancing wheat yield. In this study, we discovered that S. sclerotiorum treatment increased the diversity of the soil fungal and bacterial community in rhizosphere soil, while the diversity of the fungal community was obviously decreased in the wheat root. More importantly, the relative abundance of potential PGPR and bio-control agents increased significantly in the S. sclerotiorum-treated wheat rhizosphere soil. The importance of this work is that schizotrophic S. sclerotiorum promotes wheat growth and enhances resistance against fungal diseases via changes in the structure of the root and rhizosphere microbiome.}, }
@article {pmid37212689, year = {2023}, author = {Kehrmann, J and Koch, F and Zumdick, S and Höwner, A and Best, L and Masshöfer, L and Scharfenberg, S and Zeschnigk, M and Becker, JC and Schadendorf, D and Buer, J and Roesch, A}, title = {Reduced Staphylococcus Abundance Characterizes the Lesional Microbiome of Actinic Keratosis Patients after Field-Directed Therapies.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0440122}, doi = {10.1128/spectrum.04401-22}, pmid = {37212689}, issn = {2165-0497}, abstract = {Skin microbiome dysbiosis with a Staphylococcus overabundance is a feature of actinic keratosis (AK) and squamous skin carcinoma (SCC) patients. The impact of lesion-directed treatments for AK lesions such as diclofenac (DIC) and cold atmospheric plasma (CAP) on the lesional microbiome is not established. We studied 321 skin microbiome samples of 59 AK patients treated with DIC 3% gel versus CAP. Microbial DNA from skin swabs taken before start of treatment (week 0), at the end of the treatment period (week 24), and 3 months after end of treatment (week 36) was analyzed after sequencing the V3/V4 region of the 16S rRNA gene. The relative abundance of S. aureus was scrutinized by a tuf gene specific TaqMan PCR assay. The total bacterial load and both, relative and absolute abundance of Staphylococcus genus was reduced upon both therapies at week 24 and 36 compared to week 0. Notably, the lesional microbiome of patients responding to CAP therapy at week 24 was characterized by an increased relative abundance of Corynebacterium genus compared to nonresponders. A higher relative abundance of Staphylococcus aureus at week 36 was a feature of patients classified as nonresponders for both treatments 12 weeks after therapy completion. The reduction of the Staphylococcus abundance after treatment of AK lesions and alterations linked to treatment response encourage further studies for investigation of the role of the skin microbiome for both, the carcinogenesis of epithelial skin cancer and its function as predictive therapeutic biomarker in AK. IMPORTANCE The relevance of the skin microbiome for development of actinic keratosis (AK), its progression into squamous skin cancer, and for field-directed treatment response is unknown. An overabundance of staphylococci characterizes the skin microbiome of AK lesions. In this study, analyses of the lesional microbiome from 321 samples of 59 AK patients treated with diclophenac gel versus cold atmospheric plasma (CAP) revealed a reduced total bacterial load and reduced relative and absolute Staphylococcus genus abundance upon both treatments. A higher relative Corynebacterium abundance was a feature of patients classified as responders at the end of CAP-treatment period (week 24) compared with nonresponders and the Staphylococcus aureus abundance of patients classified as responders 3 months after treatment completion was significantly lower than in nonresponders. The alterations of the skin microbiome upon AK treatment encourage further investigations for establishing its role for carcinogenesis and its function as predictive biomarker in AK.}, }
@article {pmid37212661, year = {2023}, author = {Motta, EVS and Arnott, RLW and Moran, NA}, title = {Caffeine Consumption Helps Honey Bees Fight a Bacterial Pathogen.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0052023}, doi = {10.1128/spectrum.00520-23}, pmid = {37212661}, issn = {2165-0497}, abstract = {Caffeine has long been used as a stimulant by humans. Although this secondary metabolite is produced by some plants as a mechanism of defense against herbivores, beneficial or detrimental effects of such consumption are usually associated with dose. The Western honey bee, Apis mellifera, can also be exposed to caffeine when foraging at Coffea and Citrus plants, and low doses as are found in the nectar of these plants seem to boost memory learning and ameliorate parasite infection in bees. In this study, we investigated the effects of caffeine consumption on the gut microbiota of honey bees and on susceptibility to bacterial infection. We performed in vivo experiments in which honey bees, deprived of or colonized with their native microbiota, were exposed to nectar-relevant concentrations of caffeine for a week, then challenged with the bacterial pathogen Serratia marcescens. We found that caffeine consumption did not impact the gut microbiota or survival rates of honey bees. Moreover, microbiota-colonized bees exposed to caffeine were more resistant to infection and exhibited increased survival rates compared to microbiota-colonized or microbiota-deprived bees only exposed to the pathogen. Our findings point to an additional benefit of caffeine consumption in honey bee health by protecting against bacterial infections. IMPORTANCE The consumption of caffeine is a remarkable feature of the human diet. Common drinks, such as coffee and tea, contain caffeine as a stimulant. Interestingly, honey bees also seem to like caffeine. They are usually attracted to the low concentrations of caffeine found in nectar and pollen of Coffea plants, and consumption improves learning and memory retention, as well as protects against viruses and fungal parasites. In this study, we expanded these findings by demonstrating that caffeine can improve survival rates of honey bees infected with Serratia marcescens, a bacterial pathogen known to cause sepsis in animals. However, this beneficial effect was only observed when bees were colonized with their native gut microbiota, and caffeine seemed not to directly affect the gut microbiota or survival rates of bees. Our findings suggest a potential synergism between caffeine and gut microbial communities in protection against bacterial pathogens.}, }
@article {pmid37212579, year = {2023}, author = {Hubbard, CJ and Harrison, JG and McMinn, R and Bennett Ponsford, JC and Maignien, L and Ewers, B and Weinig, C}, title = {Rhizosphere microbial community composition shifts diurnally and in response to natural variation in host clock phenotype.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0148721}, doi = {10.1128/msystems.01487-21}, pmid = {37212579}, issn = {2379-5077}, abstract = {Plant-associated microbial assemblages are known to shift at time scales aligned with plant phenology, as influenced by the changes in plant-derived nutrient concentrations and abiotic conditions observed over a growing season. But these same factors can change dramatically in a sub24 hr period, and it is poorly understood how such diel cycling may influence plant-associated microbiomes. Plants respond to the change from day to night via mechanisms collectively referred to as the internal "clock," and clock phenotypes are associated with shifts in rhizosphere exudates and other changes that we hypothesize could affect rhizosphere microbes. The mustard Boechera stricta has wild populations that contain multiple clock phenotypes of either a 21 or a 24 hr cycle. We grew plants of both phenotypes (two genotypes per phenotype) in incubators that simulated natural diel cycling or that maintained constant light and temperature. Under both cycling and constant conditions, the extracted DNA concentration and the composition of rhizosphere microbial assemblages differed between time points, with daytime DNA concentrations often triple what were observed at night and microbial community composition differing by, for instance, up to 17%. While we found that plants of different genotypes were associated with variation in rhizosphere assemblages, we did not see an effect on soil conditioned by a particular host plant circadian phenotype on subsequent generations of plants. Our results suggest that rhizosphere microbiomes are dynamic at sub24 hr periods, and those dynamics are shaped by diel cycling in host plant phenotype.IMPORTANCEWe find that the rhizosphere microbiome shifts in composition and extractable DNA concentration in sub24 hr periods as influenced by the plant host's internal clock. These results suggest that host plant clock phenotypes could be an important determinant of variation in rhizosphere microbiomes.}, }
@article {pmid37212334, year = {2023}, author = {Rosário, A and Sousa, A and Varandas, T and Marinho-Dias, J and Medeiros, R and Martins, G and Monteiro, P and Sousa, H}, title = {Impact of cervicovaginal microbiome on the risk of cervical abnormalities development.}, journal = {Journal of medical virology}, volume = {95}, number = {5}, pages = {e28762}, doi = {10.1002/jmv.28762}, pmid = {37212334}, issn = {1096-9071}, abstract = {The vaginal microbiome has emerged as potentially influencing the natural history of Human Papillomavirus (HPV) infections and their clinical impact. We aimed to characterize the vaginal microbiome in samples from 807 high-risk HPVs (Hr-HPV) positive women with a mean age of 41.45 ± 10.79 years who participated in the Regional Cervical Cancer Screening Program from the Northern Region of Portugal. Microbiome analysis was performed with commercial kits for the detection of 21 microorganisms. The most frequent microorganisms were Ureaplasma parvum (52.5%), Gardnerella vaginalis (GV) (34.5%), Atopobium vaginae (AV) (32.6%), Lacto (30.7%), and Mycoplasma hominis (MH) (23.5%). The distribution according to age reveals that MH, Mega1, GV, BVab2, AV, and Mob were more prevalent in women older than 41 years of age (p < 0.050), while Lacto is significantly decreased in this group (23.5% vs. 39.4%, p < 0.001; RR = 0.47). The risk analysis showed that Hr-HPV-16/-18 and Hr-HPV-9val genotypes are associated with an increased risk of developing cervical abnormalities, while Lacto (p < 0.001; odd ratio [OR] = 0.33), GV (p = 0.0111; OR = 0.41), AV (p = 0.033; OR = 0.53) and Mob (p = 0.022; OR = 0.29) are associated with protection. Similar results were found for the risk of development atypical squamous cells cannot exclude HSIL/high-grade squamous intraepithelial lesion. Overall, the multivariate analysis confirmed that lactobacillus and bacteria associated with bacterial vaginosis (GV, AV, and Mob) are associated with protection against the development of cervical abnormalities. This study provides important data to be included in the future management of risk stratification for Hr-HPV-positive women.}, }
@article {pmid37212075, year = {2023}, author = {Brown, EL and Essigmann, HT and Hoffman, KL and Alexander, A and Newmark, M and Jiang, ZD and Ocampo, JS and Schiess, MC and Hanis, CL and DuPont, HL}, title = {IgA-Biome Profiles Correlate with Clinical Parkinson's Disease Subtypes.}, journal = {Journal of Parkinson's disease}, volume = {}, number = {}, pages = {}, doi = {10.3233/JPD-230066}, pmid = {37212075}, issn = {1877-718X}, abstract = {BACKGROUND: Parkinson's disease is a heterogeneous neurodegenerative disorder with distinctive gut microbiome patterns suggesting that interventions targeting the gut microbiota may prevent, slow, or reverse disease progression and severity.<br><br>OBJECTIVE: Because secretory IgA (SIgA) plays a key role in shaping the gut microbiota, characterization of the IgA-Biome of individuals classified into either the akinetic rigid (AR) or tremor dominant (TD) Parkinson's disease clinical subtypes was used to further define taxa unique to these distinct clinical phenotypes.<br><br>METHODS: Flow cytometry was used to separate IgA-coated and -uncoated bacteria from stool samples obtained from AR and TD patients followed by amplification and sequencing of the V4 region of the 16&#x200a;S rDNA gene on the MiSeq platform (Illumina).<br><br>RESULTS: IgA-Biome analyses identified significant alpha and beta diversity differences between the Parkinson's disease phenotypes and the Firmicutes/Bacteroides ratio was significantly higher in those with TD compared to those with AR. In addition, discriminant taxa analyses identified a more pro-inflammatory bacterial profile in the IgA&#xa0;+ fraction of those with the AR clinical subclass compared to IgA-Biome analyses of those with the TD subclass and with the taxa identified in the unsorted control samples.<br><br>CONCLUSION: IgA-Biome analyses underscores the importance of the host immune response in shaping the gut microbiome potentially affecting disease progression and presentation. In the present study, IgA-Biome analysis identified unique proinflammatory microbial signature in the IgA&#xa0;+ fraction of those with AR that would have otherwise been undetected using conventional microbiome analysis approaches.}, }
@article {pmid37211869, year = {2023}, author = {Wang, L and Lu, J and Yang, Y and Zhao, Y and Wang, P and Jiao, J and Zheng, H}, title = {Mechanism of cognitive impairment induced by d-galactose and l-glutamate through gut-brain interaction in tree shrews.}, journal = {Synapse (New York, N.Y.)}, volume = {}, number = {}, pages = {e22274}, doi = {10.1002/syn.22274}, pmid = {37211869}, issn = {1098-2396}, abstract = {d-Galactose (d-gal) and l-glutamate (l-glu) impair learning and memory. The mechanism of interaction between the gut microbiome and brain remains unclear. In this study, a model of cognitive impairment was induced in tree shrews by intraperitoneal (ip) injection of d-gal (600 mg/kg/day), intragastric (ig) administration with l-glu (2000 mg/kg/day), and the combination of d-gal (ip, 600 mg/kg/day) and l-glu (ig, 2000 mg/kg/day). The cognitive function of tree shrews was tested by the Morris water maze method. The expression of Aβ1-42 proteins, the intestinal barrier function proteins occludin and P-glycoprotein (P-gp), and the inflammatory factors NF-κB, TLR2, and IL-18 was determined by immunohistochemistry. The gut microbiome was analyzed by 16SrRNA high-throughput sequencing. After administering d-gal and l-glu, the escape latency increased (p < .01), and the times of crossing the platform decreased (p < .01). These changes were greater in the combined administration of d-gal and l-glu (p < .01). The expression of Aβ1-42 was higher in the perinuclear region of the cerebral cortex (p < .01) and intestinal cell (p < .05). There was a positive correlation between the cerebral cortex and intestinal tissue. Moreover, the expression of NF-κB, TLR2, IL-18, and P-gp was higher in the intestine (p < .05), while the expression of occludin and the diversity of gut microbes were lower, which altered the biological barrier of intestinal mucosal cells. This study indicated that d-gal and l-glu could induce cognitive impairment, increase the expression of Aβ1-42 in the cerebral cortex and intestinal tissue, decrease the gut microbial diversity, and alter the expression of inflammatory factors in the mucosal intestines. The dysbacteriosis may produce inflammatory cytokines to modulate neurotransmission, causing the pathogenesis of cognitive impairment. This study provides a theoretical basis to explore the mechanism of learning and memory impairment through the interaction of microbes in the gut and the brain.}, }
@article {pmid37211511, year = {2023}, author = {Robinson, JM and Breed, MF}, title = {The aerobiome-health axis: a paradigm shift in bioaerosol thinking.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2023.04.007}, pmid = {37211511}, issn = {1878-4380}, abstract = {Historically, a primary aim of bioaerosol research has been to understand and prevent 'unhealthy' human exposures to pathogens and allergens. However, there has been a recent paradigm shift in thinking about bioaerosols. Exposure to a diverse aerobiome - the microbiome of the air - is now considered necessary to be healthy.}, }
@article {pmid37211386, year = {2023}, author = {Zhang, X and Xu, W and Zhong, W and Zhang, W and Yang, C and Duan, L and Niu, H and Dong, Y and Liu, T and Xia, S and Wang, B}, title = {Exploring the links between gut microbiome changes and irritable bowel syndrome in Han populations in the Tibetan Plateau.}, journal = {Journal of Zhejiang University. Science. B}, volume = {}, number = {}, pages = {1-16}, doi = {10.1631/jzus.B2200509}, pmid = {37211386}, issn = {1862-1783}, abstract = {The gut microbiome shows changes under a plateau environment, while the disbalance of intestinal microbiota plays an important role in the pathogenesis of irritable bowel syndrome (IBS); however, the relationship between the two remains unexplored. In this work, we followed up a healthy cohort for up to a year before and after living in a plateau environment and performed 16S ribosomal RNA (rRNA) sequencing analysis of their fecal samples. Through evaluating the participants' clinical symptoms, combined with an IBS questionnaire, we screened the IBS sub-population in our cohort. The sequencing results showed that a high-altitude environment could lead to changes in the diversity and composition of gut flora. In addition, we found that the longer the time volunteers spent in the plateau environment, the more similar their gut microbiota composition and abundance became compared to those before entering the plateau, and IBS symptoms were significantly alleviated. Therefore, we speculated that the plateau may be a special environment that induces IBS. The taxonomic units g_Alistipes, g_Oscillospira, and s_Ruminococcus_torques, which had been proved to play important roles in IBS pathogenesis, were also abundant in the IBS cohort at high altitudes. Overall, the disbalance of gut microbiota induced by the plateau environment contributed to the high frequency of IBS and the psychosocial abnormalities associated with IBS. Our results prompt further research to elucidate the relevant mechanism.}, }
@article {pmid37211280, year = {2023}, author = {Chow, EWL and Mei Pang, L and Wang, Y}, title = {Impact of the host microbiota on fungal infections: new possibilities for intervention?.}, journal = {Advanced drug delivery reviews}, volume = {}, number = {}, pages = {114896}, doi = {10.1016/j.addr.2023.114896}, pmid = {37211280}, issn = {1872-8294}, abstract = {Many human fungal pathogens are opportunistic. They are primarily benign residents of the human body and only become infectious when the host's immunity and microbiome are compromised. Bacteria dominate the human microbiome, playing an essential role in keeping fungi harmless and acting as the first line of defense against fungal infection. The Human Microbiome Project, launched by NIH in 2007, has stimulated extensive investigation and significantly advanced our understanding of the molecular mechanisms governing the interaction between bacteria and fungi, providing valuable insights for developing future antifungal strategies by exploiting the interaction. This review summarizes recent progress in this field and discusses new possibilities and challenges. We must seize the opportunities presented by researching bacterial-fungal interplay in the human microbiome to address the global spread of drug-resistant fungal pathogens and the drying pipelines of effective antifungal drugs.}, }
@article {pmid37211250, year = {2023}, author = {Ridlon, JM and Daniel, SL and Gaskins, HR}, title = {The Hylemon-Björkhem Pathway of Bile Acid 7-Dehydroxylation: History, Biochemistry, and Microbiology.}, journal = {Journal of lipid research}, volume = {}, number = {}, pages = {100392}, doi = {10.1016/j.jlr.2023.100392}, pmid = {37211250}, issn = {1539-7262}, abstract = {Bile acids are detergents derived from cholesterol that function to solubilize dietary lipids, remove cholesterol from the body, and act as nutrient signaling molecules in numerous tissues with functions in the liver and gut being the best understood. Studies in the early 20th century established the structures of bile acids, and by mid-century the application of gnotobiology to bile acids allowed differentiation of host-derived "primary" bile acids from "secondary bile acids" generated by host-associated microbiota. In 1960, radiolabeling studies in rodent models led to determination of the stereochemistry of the bile acid 7-dehydration reaction. A two-step mechanism was proposed, which we have termed the Samuelsson-Bergström model, to explain the formation of deoxycholic acid. Subsequent studies with humans, rodents, and cell extracts of Clostridium scindens VPI 12708 led to the realization that bile acid 7-dehydroxylation is a result of a multi-step, bifurcating pathway, that we have named the Hylemon-Björkhem Pathway. Due to the importance of hydrophobic secondary bile acids, and the increasing measurement of microbial bai genes encoding the enzymes that produce them in stool metagenome studies, it is important to understand their origin.}, }
@article {pmid37211183, year = {2023}, author = {Yokoyama, D and Kikuchia, J}, title = {Inferring microbial community assembly in an urban river basin through geo-multi-omics and phylogenetic bin-based null-model analysis of surface water.}, journal = {Environmental research}, volume = {}, number = {}, pages = {116202}, doi = {10.1016/j.envres.2023.116202}, pmid = {37211183}, issn = {1096-0953}, abstract = {Understanding the community assembly process is a central issue in microbial ecology. In this study, we analyzed the community assembly of particle-associated (PA) and free-living (FL) surface water microbiomes in 54 sites from the headstream to the river mouth of an urban river in Japan, the river basin of which has the highest human population density in the country. Analyses were conducted from two perspectives: (1) analysis of deterministic processes considering only environmental factors using a geo-multi-omics dataset and (2) analysis of deterministic and stochastic processes to estimate the contributions of heterogeneous selection (HeS), homogeneous selection (HoS), dispersal limitation (DL), homogenizing dispersal (HD), and drift (DR) as community assembly processes using a phylogenetic bin-based null model. The variation in microbiomes was successfully explained from a deterministic perspective by environmental factors, such as organic matter-related, nitrogen metabolism, and salinity-related parameters, using multivariate statistical analysis, network analysis, and habitat prediction. In addition, we demonstrated the dominance of stochastic processes (DL, HD, and DR) over deterministic processes (HeS and HoS) in community assembly from both deterministic and stochastic perspectives. Our analysis revealed that as the distance between two sites increased, the effect of HoS sharply decreased while the effect of HeS increased, particularly between upstream and estuary sites, indicating that the salinity gradient could potentially enhance the contribution of HeS to community assembly. Our study highlights the importance of both stochastic and deterministic processes in community assembly of PA and FL surface water microbiomes in urban riverine ecosystems.}, }
@article {pmid37211108, year = {2023}, author = {Cui, J and Yi, Z and Chen, D and Fu, Y and Liu, H}, title = {Microgravity stress alters bacterial community assembly and co-occurrence networks during wheat seed germination.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164147}, doi = {10.1016/j.scitotenv.2023.164147}, pmid = {37211108}, issn = {1879-1026}, abstract = {Bacterial interactions occurring on and around seeds are integral to plant fitness, health and productivity. Although seed- and plant-associated bacteria are sensitive to environmental stress, the effects of microgravity, as present during plant cultivation in space, on microbial assembly during seed germination are not clear. Here, we characterized the bacterial microbiome assembly process and mechanisms during seed germination of two wheat varieties under simulated microgravity by 16S rRNA gene amplicon sequencing and metabolome analysis. We found that the bacterial community diversity, and network complexity and stability were significantly decreased under simulated microgravity. In addition, the effects of simulated microgravity on the plant bacteriome of the two wheat varieties tended to be consistent in seedlings. At this stage, the relative abundance of Oxalobacteraceae, Paenibacillaceae, Xanthomonadaceae, Lachnospiraceae, Sphingomonadaceae and Ruminococcaceae decreased, while the relative abundance of Enterobacteriales increased under simulated microgravity. Analysis of predicted microbial function revealed that simulated microgravity exposure leads to lower sphingolipid signaling and calcium signaling pathways. We also found that simulated microgravity drove the strengthening of deterministic processes in microbial community assembly. Importantly, some specific metabolites exhibited significant changes under simulated microgravity, suggesting that bacteriome assembly is mediated, at least in part, by metabolites altered by microgravity. The data we present here moves us closer to a holistic understanding of the plant bacteriome under microgravity stress at plant emergence, and provides a theoretical basis for the precise utilization of microorganisms in microgravity to improve plant adaptation to the challenge of cultivation in space.}, }
@article {pmid37211000, year = {2023}, author = {Chen, X and Cheng, Y and Tian, X and Li, J and Ying, X and Zhao, Q and Wang, M and Liu, Y and Qiu, Y and Yan, X and Ren, X}, title = {Urinary microbiota and metabolic signatures associated with inorganic arsenic-induced early bladder lesions.}, journal = {Ecotoxicology and environmental safety}, volume = {259}, number = {}, pages = {115010}, doi = {10.1016/j.ecoenv.2023.115010}, pmid = {37211000}, issn = {1090-2414}, abstract = {Inorganic arsenic (iAs) contamination in drinking water is a global public health problem, and exposure to iAs is a known risk factor for bladder cancer. Perturbation of urinary microbiome and metabolome induced by iAs exposure may have a more direct effect on the development of bladder cancer. The aim of this study was to determine the impact of iAs exposure on urinary microbiome and metabolome, and to identify microbiota and metabolic signatures that are associated with iAs-induced bladder lesions. We evaluated and quantified the pathological changes of bladder, and performed 16S rDNA sequencing and mass spectrometry-based metabolomics profiling on urine samples from rats exposed to low (30 mg/L NaAsO2) or high (100 mg/L NaAsO2) iAs from early life (in utero and childhood) to puberty. Our results showed that iAs induced pathological bladder lesions, and more severe effects were noticed in the high-iAs group and male rats. Furthermore, six and seven featured urinary bacteria genera were identified in female and male offspring rats, respectively. Several characteristic urinary metabolites, including Menadione, Pilocarpine, N-Acetylornithine, Prostaglandin B1, Deoxyinosine, Biopterin, and 1-Methyluric acid, were identified significantly higher in the high-iAs groups. In addition, the correlation analysis demonstrated that the differential bacteria genera were highly correlated with the featured urinary metabolites. Collectively, these results suggest that exposure to iAs in early life not only causes bladder lesions, but also perturbs urinary microbiome composition and associated metabolic profiles, which shows a strong correlation. Those differential urinary genera and metabolites may contribute to bladder lesions, suggesting a potential for development of urinary biomarkers for iAs-induced bladder cancer.}, }
@article {pmid37210851, year = {2023}, author = {Vercelli, D}, title = {From Amish farm dust to bacterial lysates: The long and winding road to protection from allergic disease.}, journal = {Seminars in immunology}, volume = {68}, number = {}, pages = {101779}, doi = {10.1016/j.smim.2023.101779}, pmid = {37210851}, issn = {1096-3618}, abstract = {Allergic diseases typically begin in early life and can impose a heavy burden on children and their families. Effective preventive measures are currently unavailable but may be ushered in by studies on the "farm effect", the strong protection from asthma and allergy found in children born and raised on traditional farms. Two decades of epidemiologic and immunologic research have demonstrated that this protection is provided by early and intense exposure to farm-associated microbes that target primarily innate immune pathways. Farm exposure also promotes timely maturation of the gut microbiome, which mediates a proportion of the protection conferred by the farm effect. Current research seeks to identify allergy-protective compounds from traditional farm environments, but standardization and regulation of such substances will likely prove challenging. On the other hand, studies in mouse models show that administration of standardized, pharmacological-grade lysates of human airway bacteria abrogates allergic lung inflammation by acting on multiple innate immune targets, including the airway epithelium/IL-33/ILC2 axis and dendritic cells whose Myd88/Trif-dependent tolerogenic reprogramming is sufficient for asthma protection in adoptive transfer models. To the extent that these bacterial lysates mimic the protective effects of natural exposure to microbe-rich environments, these agents might provide an effective tool for prevention of allergic disease.}, }
@article {pmid37210808, year = {2023}, author = {Lamichhane, S and Härkönen, T and Vatanen, T and Hyötyläinen, T and Knip, M and Orešič, M}, title = {Impact of exposure to per- and polyfluoroalkyl substances on fecal microbiota composition in mother-infant dyads.}, journal = {Environment international}, volume = {176}, number = {}, pages = {107965}, doi = {10.1016/j.envint.2023.107965}, pmid = {37210808}, issn = {1873-6750}, abstract = {There is growing evidence suggesting that chemical exposure alters gut microbiota composition. However, not much is known about the impact of per- and polyfluoroalkyl substances (PFAS) on the gut microbial community. Here, in a mother-infant study, we set out to identify the gut bacterial species that associate with chemical exposure before (maternal) and after (maternal, infant) birth. Paired serum and stool samples were collected from mother-infant dyads (n = 30) in a longitudinal setting. PFAS were quantified in maternal serum to examine their associations with the microbial compositions (determined by shotgun metagenomic sequencing) in mothers and infants. High maternal exposure to PFAS was consistently associated with increased abundance of Methanobrevibacter smithii in maternal stool. Among individual PFAS compounds, PFOS and PFHpS showed the strongest association with M. smithii. However, maternal total PFAS exposure associated only weakly with the infant microbiome. Our findings suggest that PFAS exposure affects the composition of the adult gut microbiome.}, }
@article {pmid37210594, year = {2023}, author = {Murray, N and Al Khalaf, S and Bastiaanssen, TFS and Kaulmann, D and Lonergan, E and Cryan, JF and Clarke, G and Khashan, AS and O'Connor, K}, title = {Compositional and Functional Alterations in Intestinal Microbiota in Patients with Psychosis or Schizophrenia: A Systematic Review and Meta-analysis.}, journal = {Schizophrenia bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1093/schbul/sbad049}, pmid = {37210594}, issn = {1745-1701}, abstract = {BACKGROUND AND HYPOTHESIS: Intestinal microbiota is intrinsically linked to human health. Evidence suggests that the composition and function of the microbiome differs in those with schizophrenia compared with controls. It is not clear how these alterations functionally impact people with schizophrenia. We performed a systematic review and meta-analysis to combine and evaluate data on compositional and functional alterations in microbiota in patients with psychosis or schizophrenia.<br><br>STUDY DESIGN: Original studies involving humans and animals were included. The electronic databases PsycINFO, EMBASE, Web of Science, PubMed/MEDLINE, and Cochrane were systematically searched and quantitative analysis performed.<br><br>STUDY RESULTS: Sixteen original studies met inclusion criteria (1376 participants: 748 cases and 628 controls). Ten were included in the meta-analysis. Although observed species and Chao 1 show a decrease in diversity in people with schizophrenia compared with controls (SMD = -0.14 and -0.66 respectively), that did not reach statistical significance. We did not find evidence for variations in richness or evenness of microbiota between patients and controls overall. Differences in beta diversity and consistent patterns in microbial taxa were noted across studies. We found increases in Bifidobacterium, Lactobacillus, and Megasphaera in schizophrenia groups. Variations in brain structure, metabolic pathways, and symptom severity may be associated with compositional alterations in the microbiome. The heterogeneous design of studies complicates a similar evaluation of functional readouts.<br><br>CONCLUSIONS: The microbiome may play a role in the etiology and symptomatology of schizophrenia. Understanding how the implications of alterations in microbial genes for symptomatic expression and clinical outcomes may contribute to the development of microbiome targeted interventions for psychosis.}, }
@article {pmid37169132, year = {2023}, author = {Medina-Rodriguez, EM and Han, D and Lowell, J and Beurel, E}, title = {Stress promotes the infiltration of peripheral immune cells to the brain.}, journal = {Brain, behavior, and immunity}, volume = {111}, number = {}, pages = {412-423}, doi = {10.1016/j.bbi.2023.05.003}, pmid = {37169132}, issn = {1090-2139}, abstract = {Immune cells and the brain have a privileged interaction. Here, we report changes in the hippocampal immune microenvironment at the single cell level after stress, uncovering the tight orchestration of immune cell infiltration into the hippocampus after stress to maintain homeostasis. We show the distribution of several immune cell types in the hippocampus associated with their susceptibility or resilience to the learned helplessness paradigm in a sex- and microbiota-dependent manner using single-cell RNA sequencing and bioinformatic tools, flow cytometry, and immunofluorescence. We uncovered the presence of tissue-resident memory T cells that accumulate over time in the hippocampus of learned helpless mice, and the presence of CD74-expressing myeloid cells. These cells were found by a knockdown approach to be critical to induce resilience to learned helplessness. Altogether, these findings provide a novel overview of the neuro-immune repertoire and its impact on the landscape of the hippocampus after learned helplessness.}, }
@article {pmid37070751, year = {2023}, author = {Fekete, E and Buret, AG}, title = {The role of mucin O-glycans in microbiota dysbiosis, intestinal homeostasis, and host-pathogen interactions.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {324}, number = {6}, pages = {G452-G465}, doi = {10.1152/ajpgi.00261.2022}, pmid = {37070751}, issn = {1522-1547}, abstract = {Mucin O-linked glycans are important mediators of host-microbiota-pathogen interactions in the gastrointestinal tract. The major component of intestinal mucus, the MUC2 mucin, is densely glycosylated, with up to 80% of its weight-to-volume ratio represented by O-linked glycans. Glycosylation of secretory gel-forming mucins has an enormous impact on intestinal barrier function, microbial metabolism, and mucus colonization by both pathogenic and commensal microbes. Mucin O-glycans and glycan-derived sugars may be degraded and used as a nutrient source and may regulate microbial gene expression and virulence. Short-chain fatty acids, produced as a by-product of glycan fermentation, can regulate host immunity and goblet cell activity and are important for host-microbe homeostasis. Mucin glycans may also act as microbial binding sites, influencing intestinal colonization and translocation through the mucus gel barrier. Recent findings indicate that alterations to mucin glycosylation impact the susceptibility of mucins to degradation, resulting in altered barrier function and intestinal permeability. Alterations to mucin glycosylation patterns are frequently observed during intestinal infection and inflammation and have been implicated in microbiota dysbiosis and expansion of pathobionts. Recent work has demonstrated that these alterations can play key roles in disease pathogenesis. The precise mechanisms remain obscure. This review highlights the important roles of O-linked glycans in host-microbe interactions and disease pathogenesis in the context of intestinal infections.}, }
@article {pmid37210515, year = {2023}, author = {Leleiwi, I and Rodriguez-Ramos, J and Shaffer, M and Sabag-Daigle, A and Kokkinias, K and Flynn, RM and Daly, RA and Kop, LFM and Solden, LM and Ahmer, BMM and Borton, MA and Wrighton, KC}, title = {Exposing new taxonomic variation with inflammation - a murine model-specific genome database for gut microbiome researchers.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {114}, pmid = {37210515}, issn = {2049-2618}, support = {R01AI143288/NH/NIH HHS/United States ; R01AI143288/NH/NIH HHS/United States ; R01AI143288/NH/NIH HHS/United States ; R01AI143288/NH/NIH HHS/United States ; R01AI143288/NH/NIH HHS/United States ; R01AI143288/NH/NIH HHS/United States ; R01AI143288/NH/NIH HHS/United States ; R01AI143288/NH/NIH HHS/United States ; R01AI143288/NH/NIH HHS/United States ; R01AI143288/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: The murine CBA/J mouse model widely supports immunology and enteric pathogen research. This model has illuminated Salmonella interactions with the gut microbiome since pathogen proliferation does not require disruptive pretreatment of the native microbiota, nor does it become systemic, thereby representing an analog to gastroenteritis disease progression in humans. Despite the value to broad research communities, microbiota in CBA/J mice are not represented in current murine microbiome genome catalogs.<br><br>RESULTS: Here we present the first microbial and viral genomic catalog of the CBA/J murine gut microbiome. Using fecal microbial communities from untreated and Salmonella-infected, highly inflamed mice, we performed genomic reconstruction to determine the impacts on gut microbiome membership and functional potential. From high depth whole community sequencing (~&#x2009;42.4 Gbps/sample), we reconstructed 2281 bacterial and 4516 viral draft genomes. Salmonella challenge significantly altered gut membership in CBA/J mice, revealing 30 genera and 98 species that were conditionally rare and unsampled in non-inflamed mice. Additionally, inflamed communities were depleted in microbial genes that modulate host anti-inflammatory pathways and enriched in genes for respiratory energy generation. Our findings suggest decreases in butyrate concentrations during Salmonella infection corresponded to reductions in the relative abundance in members of the Alistipes. Strain-level comparison of CBA/J microbial genomes to prominent murine gut microbiome databases identified newly sampled lineages in this resource, while comparisons to human gut microbiomes extended the host relevance of dominant CBA/J inflammation-resistant strains.<br><br>CONCLUSIONS: This CBA/J microbiome database provides the first genomic sampling of relevant, uncultivated microorganisms within the gut from this widely used laboratory model. Using this resource, we curated a functional, strain-resolved view on how Salmonella remodels intact murine gut communities, advancing pathobiome understanding beyond inferences from prior amplicon-based approaches. Salmonella-induced inflammation suppressed Alistipes and other dominant members, while rarer commensals like Lactobacillus and Enterococcus endure. The rare and novel species sampled across this inflammation gradient advance the utility of this microbiome resource to benefit the broad research needs of the CBA/J scientific community, and those using murine models for understanding the impact of inflammation on the gut microbiome more generally. Video Abstract.}, }
@article {pmid37210496, year = {2023}, author = {Li, H and Xiao, HY and Yuan, LP and Yan, B and Pan, Y and Tian, PP and Zhang, WJ}, title = {Protective effect of L-pipecolic acid on constipation in C57BL/6 mice based on gut microbiome and serum metabolomic.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {144}, pmid = {37210496}, issn = {1471-2180}, abstract = {BACKGROUND: Functional constipation (FC) in children affects their growth, development and quality of life. L-pipecolic acid (L-PA) was decreased in FC children based on gut microbiome and serum metabolomic. In this study, loperamide-induced constipation in mice was used to evaluate the effects of L-PA on constipated mice.<br><br>METHOD: 26 FC and 28 healthy children were recruited. Stool samples and serum samples were subjected to 16S rDNA sequencing and ultra-performance liquid chromatography/quadrupole time of flight (UPLC-Q/TOF-MS) approach, respectively. A loperamide-induced mouse constipation model was developed, and all mice were randomly divided into control (Con), loperamide (Lop) and L-PA (Lop&#x2009;+&#x2009;L-PA) treatment groups (6 mice per group). The mice in the Lop&#x2009;+&#x2009;L-PA group were given L-PA (250&#xa0;mg/kg, once a day) and loperamide; the Lop group was given loperamide for 1 week, and the Con group was given saline. The fecal parameters and intestinal motility of mice in each group were detected. serum 5-HT levels and colon 5-HT expression were detected by ELISA and immunohistochemistry, respectively; qRT-PCR was used to detect the expression of AQP3 and 5-HT4R mRNA in each group.<br><br>RESULTS: 45 differential metabolites and 18 significantly different microbiota were found in FC children. The &#x3b1; and &#x3b2; diversity of gut microbiota in FC children was significantly reduced. Importantly, serum L-PA was significantly reduced in FC children. The KEGG pathway enrichment were mainly enriched in fatty acid biosynthesis, lysine degradation, and choline metabolism. L-PA was negatively associated with Ochrobactrum, and N6, N6, N6-trimethyl-l-lysine was positively associated with Phascolarcrobacterium. In addition, L-PA improved the fecal water content, intestinal transit rate, and increased the serum 5-HT levels in constipated mice. Moreover, L-PA increased the expression of 5-HT4R, reduced AQP3, and regulated constipation-associated genes.<br><br>CONCLUSIONS: Gut microbiota and serum metabolites were significantly altered in children with FC. The abundance of Phascolarctobacterium and Ochrobactrum and serum L-PA content were decreased in FC children. L-PA was found to alleviate the fecal water content, increase intestinal transit rate and the first black stool defecation time. L-PA improved constipation by increasing 5-HT and 5-HT4R expression while down-regulating AQP3 expression.}, }
@article {pmid37210416, year = {2023}, author = {Toyoda, A and Shibata, Y and Matsuo, Y and Terada, K and Sugimoto, H and Higashi, K and Mori, H and Ikeuchi, A and Ito, M and Kurokawa, K and Katahira, S}, title = {Diversity and compositional differences of the airborne microbiome in a biophilic indoor environment.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8179}, pmid = {37210416}, issn = {2045-2322}, abstract = {Biophilic design based on indoor planting plays an important role in human physical and mental well-being. To investigate and assess the effects of indoor planting on air quality, we sequenced 16S rRNA gene amplicons to compare the airborne bacterial microbiomes of three planting rooms before and after installing natural materials (plants, soil, water, etc.) with distinct biophilic attributes. Incorporation of indoor plantings significantly increased the taxonomic diversity of the airborne microbiome in each room, and we observed different microbiome compositions in each room. The proportional contribution of each bacterial source to the airborne microbiome in the indoor planting rooms was estimated by SourceTracker2. This analysis revealed that the proportion of airborne microbial sources (e.g., plants and soil) varied depending on the natural materials installed. Our results have important implications for indoor planting with biophilic design to control the indoor airborne microbiome.}, }
@article {pmid37210363, year = {2023}, author = {Mulakala, BK and Smith, KM and Snider, MA and Ayers, A and Honan, MC and Greenwood, SL}, title = {Use of milk proteins as biomarkers of changes in the rumen metaproteome of Holstein cows fed low fiber, high starch diets.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2022-22910}, pmid = {37210363}, issn = {1525-3198}, abstract = {Dietary levels of undegraded neutral detergent fiber (uNDF240) and rumen fermentable starch (RFS) can impact the rumen microbiome and milk composition. The objective of the study is to investigate the use of milk proteins as biomarkers of rumen microbial activity through a comparative evaluation of the rumen microbial and milk protein profiles produced by Holstein cows fed diets with varying contents of physically effective uNDF240 (peuNDF240) and RFS. Eight ruminally cannulated lactating Holstein cows were included in a larger study as part of a 4 × 4 Latin square design with 4 28-d periods to assess 4 diets varying in peuNDF240 and RFS content. For this experiment, cows received one of 2 dietary treatments: 1) low peuNDF240, high RFS (LNHR) diet or 2) high peuNDF240, low RFS (HNLR) diet. Within each period, rumen fluid samples were collected from each cow on d 26 (1400 h) and d 27 (0600 h and 1000 h), and milk samples were collected from each cow on d 25 (2030 h), d 26 (0430 h, 1230 h, and 2030 h), and d 27 (0430 h and 1230 h). Microbial proteins were isolated from each rumen fluid sample. For milk samples, milk proteins were fractionated, and the whey fraction was subsequently isolated. Isolated proteins within each rumen fluid or milk sample were isobarically labeled and analyzed by LC-MS/MS. Product ion spectra acquired from rumen fluid samples were searched using SEQUEST against 71 composite databases. In contrast, product ion spectra acquired from milk samples were searched against the Bos taurus database. Data were analyzed using the PROC MIXED procedure in SAS 9.4 to assess the impact of diet and time of sampling. To increase stringency, the false discovery rate-adjusted P-value (PFDR) was also calculated to account for multiple comparisons. Using the mixed procedure, a total of 129 rumen microbial proteins were quantified across 24 searched microbial species. Of these, the abundance of 14 proteins across 9 microbial species was impacted due to diet and diet × time interaction, including 7 proteins associated with energetics pathways. Among the 159 quantified milk proteins, the abundance of 21 proteins was impacted due to the diet and diet × time interaction. The abundance of 19 of these milk proteins was impacted due to diet × time interactions. Of these, 16 proteins had the disparity across diets at the 0430 h sampling time, including proteins involved in host defense, nutrient synthesis, and transportation, suggesting that biological shifts resulting from diet-induced rumen changes are not diurnally uniform across milkings. The concentration of lipoprotein lipase (LPL) was statistically higher in the milk from the cows fed with the LNHR diet, which was numerically confirmed with an ELISA. Further, as determined by ELISA, the LPL concentration was significantly higher in the milk from the cows fed with the LNHR diet at 0430 h sampling point, suggesting that LPL concentration may indicate dietary carbohydrate-induced ruminal changes. The results of this study suggest that diet-induced rumen changes can be reflected in milk in a diurnal pattern, further highlighting the need to consider sampling time points for using milk proteins as a representative biomarker of rumen microbial activity.}, }
@article {pmid37210004, year = {2023}, author = {Delaye, M and Rousseau, A and Mailly-Giacchetti, L and Assoun, S and Sokol, H and Neuzillet, C}, title = {Obesity, cancer, and response to immune checkpoint inhibitors: Could the gut microbiota be the mechanistic link?.}, journal = {Pharmacology &amp; therapeutics}, volume = {}, number = {}, pages = {108442}, doi = {10.1016/j.pharmthera.2023.108442}, pmid = {37210004}, issn = {1879-016X}, abstract = {Immune checkpoint inhibitors (ICI) have deeply changed the therapeutic management of a broad spectrum of solid tumors. Recent observations showed that obese patients receiving ICIs might have better outcomes than those with normal weight, while obesity was historically associated with a worse prognosis in cancer patients. Of note, obesity is associated with alterations in the gut microbiome profile, which interacts with immune and inflammatory pathways, both at the systemic and intratumoral levels. As the influence of the gut microbiota on the response to ICI has been repeatedly reported, a specific gut microbiome profile in obese cancer patients may be involved in their better response to ICI. This review summarizes recent data on the interactions between obesity, gut microbiota, and ICIs. In addition, we highlight possible pathophysiological mechanisms supporting the hypothesis that gut microbiota could be one of the links between obesity and poor response to ICIs.}, }
@article {pmid37209986, year = {2023}, author = {Zhang, M and Tang, H and Chen, Y and Chen, Z and Xu, Y and Fu, X and Sun, Y and Zhao, Z}, title = {Impact of environmental characteristics on children's gut microbiota - A pilot study in assessing the role of indoor microbiome and metabolites.}, journal = {Environmental research}, volume = {}, number = {}, pages = {116114}, doi = {10.1016/j.envres.2023.116114}, pmid = {37209986}, issn = {1096-0953}, abstract = {BACKGROUND: A diverse and balanced human gut microbiota is crucial for maintaining normal human physiological functions. However, the impact of indoor microbiome and metabolites on gut microbiota is not well understood.<br><br>METHODS: A self-administered questionnaire was used to collect information on more than 40 personal and environmental characteristics and dietary habits from 56 children in Shanghai, China. Shotgun metagenomics and untargeted liquid chromatography-mass spectrometry (LC-MS) were used to characterize the indoor microbiome and metabolomic/chemical exposure in children's living rooms. PacBio full-length 16&#x202f;S rRNA sequencing was used to characterize children's gut microbiota. Associations between environmental characteristics and gut microbiota diversity/composition were assessed using PERMANOVA and regression.<br><br>RESULTS: In total, 6247 and 318 indoor and gut microbial species and 1442 indoor metabolites were characterized. Age of children (R[2]&#x202f;=&#x202f;0.033, p&#x202f;=&#x202f;0.008), age start kindergarten (R[2]&#x202f;=&#x202f;0.029, p&#x202f;=&#x202f;0.03), living adjacent to heavy traffic (R[2]&#x202f;=&#x202f;0.031, p&#x202f;=&#x202f;0.01) and drinking soft drinks (R[2]&#x202f;=&#x202f;0.028, p&#x202f;=&#x202f;0.04) significantly impacted overall gut microbial composition, consistent with previous studies. Having pets/plants and frequent vegetable intake were positively associated with gut microbiota diversity and the Gut Microbiome Health Index (GMHI), while frequent juice and fries intake decreased gut microbiota diversity (p&#x202f;<&#x202f;0.05). The abundance of indoor Clostridia and Bacilli was positively associated with gut microbial diversity and GMHI (p&#x202f;<&#x202f;0.01). Total indoor indole derivatives and 6 indole metabolites (L-tryptophan, indole, 3-methylindole, indole-3-acetate, 5-hydroxy-L-tryptophan and indolelactic acid, p&#x202f;<&#x202f;0.05) were positively associated with the abundance of total protective gut bacteria, suggesting a potential role in promoting gut health. Neural network analysis revealed that these indole derivatives were derived from indoor microorganisms.<br><br>CONCLUSIONS: The study is the first to report associations between indoor microbiome/metabolites and gut microbiota, highlighting the potential role of indoor microbiome in shaping human gut microbiota.}, }
@article {pmid37209745, year = {2023}, author = {Núñez-Pons, L and Cunning, R and Nelson, C and Amend, A and Sogin, EM and Gates, R and Ritson-Williams, R}, title = {Hawai'ian coral holobionts reveal algal and prokaryotic host specificity, intraspecific variability in bleaching resistance, and common interspecific microbial consortia modulating thermal stress responses.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164040}, doi = {10.1016/j.scitotenv.2023.164040}, pmid = {37209745}, issn = {1879-1026}, abstract = {Historically, Hawai'i had few massive coral bleaching events, until two consecutive heatwaves in 2014-2015. Consequent mortality and thermal stress were observed in Kane'ohe Bay (O'ahu). The two most dominant local species exhibited a phenotypic dichotomy of either bleaching resistance or susceptibility (Montipora capitata and Porites compressa), while the third predominant species (Pocillopora acuta) was broadly susceptible to bleaching. In order to survey shifts in coral microbiomes during bleaching and recovery, 50 colonies were tagged and periodically monitored. Metabarcoding of three genetic markers (16S rRNA gene ITS1 and ITS2) followed by compositional approaches for community structure analysis, differential abundance and correlations for longitudinal data were used to temporally compare Bacteria/Archaea, Fungi and Symbiodiniaceae dynamics. P. compressa corals recovered faster than P. acuta and Montipora capitata. Prokaryotic and algal communities were majorly shaped by host species, and had no apparent pattern of temporal acclimatization. Symbiodiniaceae signatures were identified at the colony scale, and were often related to bleaching susceptibility. Bacterial compositions were practically constant between bleaching phenotypes, and more diverse in P. acuta and M. capitata. P. compressa's prokaryotic community was dominated by a single bacterium. Compositional approaches (via microbial balances) allowed the identification of fine-scale differences in the abundance of a consortium of microbes, driving changes by bleaching susceptibility and time across all hosts. The three major coral reef founder-species in Kane'ohe Bay revealed different phenotypic and microbiome responses after 2014-2015 heatwaves. It is difficult to forecast, a more successful strategy towards future scenarios of global warming. Differentially abundant microbial taxa across time and/or bleaching susceptibility were broadly shared among all hosts, suggesting that locally, the same microbes may modulate stress responses in sympatric coral species. Our study highlights the potential of investigating microbial balances to identify fine-scale microbiome changes, serving as local diagnostic tools of coral reef fitness.}, }
@article {pmid37209734, year = {2023}, author = {Sun, H and Xie, Z and Yang, X and Yang, B and Liao, B and Yin, J and Xiao, B}, title = {New insights into microbial and metabolite signatures of coral bleaching.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164258}, doi = {10.1016/j.scitotenv.2023.164258}, pmid = {37209734}, issn = {1879-1026}, abstract = {Coral bleaching and coral reef degradation have been severely increased due to anthropogenic impacts, especially global warming. Studies have indicated the key role of host-microbiome symbiotic relationships for the coral holobiont health and development, although not all of the mechanisms of interaction have been fully explored. Here, we explore bacterial and metabolic shifts within coral holobionts under thermal stress, and its correlation with bleaching. Our results showed obvious signs of coral bleaching after 13 days of heating treatment, and a more-complex co-occurrence network was observed in the coral-associated bacterial community of the heating group. The bacterial community and metabolites changed significantly under thermal stress, and genera Flavobacterium, Shewanella and Psychrobacter increased from <0.1 % to 43.58 %, 6.95 % and 6.35 %, respectively. Bacteria potentially associated with stress tolerance, biofilm formation and mobile elements decreased from 80.93 %, 62.15 % and 49.27 % to 56.28 %, 28.41 % and 18.76 %, respectively. The differentially expressed metabolites of corals after heating treatment, such as Cer(d18:0/17:0), 1-Methyladenosine, Trp-P-1 and Marasmal, were associated with cell cycle regulation and antioxidant properties. Our results can contribute to our current understanding on the correlations between coral-symbiotic bacteria, metabolites and the coral physiological response to thermal stress. These new insights into the metabolomics of heat-stressed coral holobionts may expand our knowledge on the mechanisms underlying bleaching.}, }
@article {pmid37209727, year = {2023}, author = {Khalaf, DM and Cruzeiro, C and Siani, R and Kublik, S and Schröder, P}, title = {Resilience of barley (Hordeum vulgare) plants upon exposure to tramadol: Implication for the root-associated bacterial community and the antioxidative plant defence system.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164260}, doi = {10.1016/j.scitotenv.2023.164260}, pmid = {37209727}, issn = {1879-1026}, abstract = {Insufficiently treated reclaimed water can act as a source of contamination by introducing recalcitrant contaminants (e.g., pharmaceutical compounds) to various water bodies and/or agricultural soils after irrigation. Tramadol (TRD) is one of these pharmaceuticals that can be detected in influents and effluents of wastewater treatment plants, at discharge points as well as in surface waters in Europe. While the uptake of TRD by plants through irrigation water has been shown, plant responses towards this compound are still unclear. Therefore, this study aims to evaluate the effects of TRD on selected plant enzymes as well as on the root bacterial community structure. A hydroponic experiment was conducted to test the effects of TRD (100 μg L[-1] TRD) on barley plants, at two harvesting time points after treatment. Accumulation of TRD in root tissues over time was observed reaching concentrations of 27.94 and 34.60 μg g[-1] FW root after 12 and 24 days of exposure, respectively. Furthermore, noticeable inductions in guaiacol peroxidase (5.47-fold), catalase (1.83-fold) and glutathione S-transferase (3.23- and 2.09-fold) were recorded in roots of TRD-treated plants compared to controls after 24 days. A significant alteration in the beta diversity of root-associated bacteria due to TRD treatment was observed. Three amplicon sequence variants assigned to Hydrogenophaga, U. Xanthobacteraceae and Pseudacidovorax were differentially abundant in TRD-treated compared to control plants at both harvesting time points. This study reveals the resilience of plants through the induction of the antioxidative system and changes in the root-associated bacterial community to cope with the TRD metabolization/detoxification process.}, }
@article {pmid37209654, year = {2023}, author = {Xiong, X and Xu, J and Yan, X and Wu, S and Ma, J and Wang, Z and He, Q and Gong, J and Rao, Y}, title = {Gut microbiome and serum metabolome analyses identify biomarkers associated with sexual maturity in quails.}, journal = {Poultry science}, volume = {102}, number = {7}, pages = {102762}, doi = {10.1016/j.psj.2023.102762}, pmid = {37209654}, issn = {1525-3171}, abstract = {Increasing evidence indicates that the gut microbiome plays an important role in host aging and sexual maturity. However, the gut microbial taxa associated with sexual maturity in quails are unknown. This study used shotgun metagenomic sequencing to identify bacterial taxa associated with sexual maturity in d 20 and d 70 quails. We found that 17 bacterial species and 67 metagenome-assembled genomes (e.g., Bacteroides spp. and Enterococcus spp.) significantly differed between the d 20 and d 70 groups, including 5 bacterial species (e.g., Enterococcus faecalis) enriched in the d 20 group and 12 bacterial species (e.g., Christensenella massiliensis, Clostridium sp. CAG:217, and Bacteroides neonati) which had high abundances in the d 70 group. The bacterial species enriched in d 20 or d 70 were key biomarkers distinguishing sexual maturity and significantly correlated with the shifts in the functional capacities of the gut microbiome. Untargeted serum metabolome analysis revealed that 5 metabolites (e.g., nicotinamide riboside) were enriched in the d 20 group, and 6 metabolites (e.g., D-ribose, stevioside, and barbituric acid) were enriched in the d 70 group. Furthermore, metabolites with high abundances in the d 20 group were significantly enriched for the KEGG pathways of arginine biosynthesis, nicotinate and nicotinamide metabolism, and lysine degradation. However, glutathione metabolism and valine, leucine and isoleucine biosynthesis were enriched in high-abundance metabolites from the d 70 group. These results provide important insights into the effects of gut microbiome and host metabolism on quail sexual maturity.}, }
@article {pmid37209652, year = {2023}, author = {Hao, G and Li, P and Huang, J and Cui, K and Liang, L and Lin, F and Lu, Z and Sun, S}, title = {Research Note: Therapeutic effect of a Salmonella phage combination on chicks infected with Salmonella Typhimurium.}, journal = {Poultry science}, volume = {102}, number = {7}, pages = {102715}, doi = {10.1016/j.psj.2023.102715}, pmid = {37209652}, issn = {1525-3171}, abstract = {Antibiotic treatment failure is increasingly encountered for the emergence of pandrug-resistant isolates, including the prototypical broad-host-range Salmonella enterica serovar (S.) Typhimurium, which mainly transmitted to humans through poultry products. In this study we explored the therapeutic potential of a Salmonella phage composition containing a virulent phage and a nonproductive phage that does not produce progeny phage against chicks infected with a pandrug-resistant S. Typhimurium strain of avian origin. After approximately 10[7] CFU of S. Typhimurium strain ST149 were administrated to chicks by intraperitoneal injection, the phage combination (∼10[8] PFU) was gavaged at 8-h, 32-h, and 54-h postinfection. At d 10 postinfection, phage treatment completely protected chicks from Salmonella-induced death compared to 91.7% survival in the Salmonella challenge group. In addition, phage treatment also greatly reduced the bacterial load in various organs, with Salmonella colonization levels decreasing more significantly in spleen and bursa than in liver and cecal contents, possibly due to higher phage titers in these immune organs. However, phages could not alleviate the decreased body weight gain and the enlargement of spleen and bursa of infected chicks. Further examination of the bacterial flora in the cecal contents of chicks found that S. Typhimurium infection caused a remarkable decrease in abundance of Clostridia vadin BB60 group and Mollicutes RF39 (the dominant genus in chicks), making Lactobacillus the dominate genus. Although phage treatment partially restored the decline of Clostridia vadin BB60 group and Mollicutes RF39 and increased abundance of Lactobacillus caused by S. Typhimurium infection, Fournierella that may aggravate intestinal inflammation became the major genus, followed by increased Escherichia-Shigella as the second dominate bacterial genus. These results suggested that successive phage treatment modulated the structural composition and abundance of bacterial communities, but failed to normalize the intestinal microbiome disrupted by S. Typhimurium infection. Phages need to be combined with other means to control the spread of S. Typhimurium in poultry.}, }
@article {pmid37209285, year = {2023}, author = {Booth, JM and Fusi, M and Marasco, R and Daffonchio, D}, title = {The microbial landscape in bioturbated mangrove sediment: A resource for promoting nature-based solutions for mangroves.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.14273}, pmid = {37209285}, issn = {1751-7915}, abstract = {Globally, soils and sediments are affected by the bioturbation activities of benthic species. The consequences of these activities are particularly impactful in intertidal sediment, which is generally anoxic and nutrient-poor. Mangrove intertidal sediments are of particular interest because, as the most productive forests and one of the most important stores of blue carbon, they provide global-scale ecosystem services. The mangrove sediment microbiome is fundamental for ecosystem functioning, influencing the efficiency of nutrient cycling and the abundance and distribution of key biological elements. Redox reactions in bioturbated sediment can be extremely complex, with one reaction creating a cascade effect on the succession of respiration pathways. This facilitates the overlap of different respiratory metabolisms important in the element cycles of the mangrove sediment, including carbon, nitrogen, sulphur and iron cycles, among others. Considering that all ecological functions and services provided by mangrove environments involve microorganisms, this work reviews the microbial roles in nutrient cycling in relation to bioturbation by animals and plants, the main mangrove ecosystem engineers. We highlight the diversity of bioturbating organisms and explore the diversity, dynamics and functions of the sediment microbiome, considering both the impacts of bioturbation. Finally, we review the growing evidence that bioturbation, through altering the sediment microbiome and environment, determining a 'halo effect', can ameliorate conditions for plant growth, highlighting the potential of the mangrove microbiome as a nature-based solution to sustain mangrove development and support the role of this ecosystem to deliver essential ecological services.}, }
@article {pmid37209162, year = {2023}, author = {Feng, S and Meng, C and Liu, Y and Yi, Y and Liang, A and Zhang, Y and Hao, Z}, title = {Bacillus licheniformis prevents and reduces anxiety-like and depression-like behaviours.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {37209162}, issn = {1432-0614}, abstract = {As common mental disorders, depression and anxiety impact people all around the world. Recent studies have found that the gut microbiome plays an important role in mental health. It is becoming possible to treat mental disorders by regulating the composition of the gut microbiota. Bacillus licheniformis is a probiotic used to treat gut diseases through balancing the gut microbiome during lasting years. Considering the role of gut microbiota in the gut-brain axis, this study used chronic unpredictable mild stress (CUMS) model rats to explore whether Bacillus licheniformis can prevent and treat depression and anxiety. We found that B. licheniformis reduced the depressive-like and anxiety-like behaviours of the rats during the CUMS process. Meanwhile, B. licheniformis changed the gut microbiota composition; increased the short chain fatty acids (SCFAs) in the colon, decreased kynurenine, norepinephrine, and glutamate levels; and increased the tryptophan, dopamine, epinephrine, and γ-aminobutyric acid (GABA) in the brain. After correlation analysis, we found Parabacteroides, Anaerostipes, Ruminococcus-2, and Blautia showed significant correlation with neurotransmitters and SCFAs, indicating the gut microbiome plays an important role in B. licheniformis reducing depressive-like behaviours. Therefore, this study suggested B. licheniformis may prevent depressive-like and anxiety-like behaviours while regulating the gut microbiota composition and increasing the SCFA levels in the colon to alter the levels of the neurotransmitters in the brain. KEY POINTS: • B. licheniformis reduced depressive-like and anxiety-like behaviours induced by the chronic unpredictable mild stress. • GABA levels in the brain are assonated with B. licheniformis regulating depressive-like and anxiety-like behaviours. • Gut microbiota composition alteration followed by metabolic changes may play a role in the GABA levels increase.}, }
@article {pmid37209081, year = {2023}, author = {Wang, N and Ding, J and Chen, Y and Zhu, Y and Zhang, L and Wei, Y and Li, J and Xu, T and Ding, GC}, title = {Bacillus velezensis BER1 enriched Flavobacterium daejeonense-like bacterium in the rhizosphere of tomato against bacterial wilt.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiad054}, pmid = {37209081}, issn = {1574-6941}, abstract = {Beneficial microorganisms can protect crop from phytopathogens, and modify rhizosphere microbiome. However, it is not well understood whether or how do rhizosphere microorganisms which respond to bio-agents contribute to disease suppression. Bacillus velezensis BER1 and tomato bacterial wilt caused by Ralstonia solanacearum were selected as models to disentangle the interactions and mechanisms in the rhizosphere. B. velezensis BER1 greatly suppressed tomato bacterial wilt by over 49.0%, reduced R. solanacearum colonization in the rhizosphere by 36.3%, and significantly enriched two Flavobacterium ASVs (1357 and 2401). A novel colony Loop-Mediated Isothermal Amplification (LAMP) assay system was developed to screen out Flavobacterium from tomato rhizosphere bacterial isolates. In vitro tests revealed that co-cultivating BER1 with Flavobacterium C45 increased biofilm formation by 18.6%. Climate chamber experiment further revealed that Flavobacterium C45 improved the control efficiency of BER1 on tomato bacterial wilt by 46.0%, decreased the colonization of R. solanacearum in the rhizosphere by 43.1% and elevated the transcription of plant defense gene PR1α in tomato by 45.4%. In summary, Flavobacterium C45 boosted the ability of B. velezensis BER1 to prevent bacterial wilt and the colonization of R. solanacearum, highlighting the importance of helper bacteria on elevating the efficiency of biological control.}, }
@article {pmid37209012, year = {2023}, author = {Arias-Moliz, MT and Ordinola-Zapata, R and Staley, C and Pérez-Carrasco, V and García-Salcedo, JA and Uroz-Torres, D and Soriano, M}, title = {Exploring the Root Canal Microbiome in Previously Treated Teeth: A Comparative Study of Diversity and Metabolic Pathways Across Two Geographical Locations.}, journal = {International endodontic journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/iej.13934}, pmid = {37209012}, issn = {1365-2591}, abstract = {AIM: To analyze and compare the root canal microbiome present in root-filled teeth of two different geographical populations, and to study their functional potential using next-a generation sequencing approach.<br><br>METHODOLOGY: Sequencing data obtained from surgical specimens from previously treated teeth with periapical bone loss from Spain and USA were included in the study. Taxa were classified using SILVA v.138 database. Differences in genera abundances among the 10 most abundant genera were evaluated using a Kruskal-Wallis test. Alpha diversity indices were calculated in mothur. The Shannon and Chao1 indices were used. Analyses of similarity (ANOSIM) to determine differences in community composition were done in mothur, with Bonferroni correction for multiple comparisons. P values <&#x2009;0.05 were considered statistically significant. Identification of enriched bacteria function prediction in the study groups (Kegg pathways) was carried out by Linear discriminant analysis Effect Size (LEfSe) via Python 3.7.6.<br><br>RESULTS: A greater alpha-diversity (Shannon and Chao1 indices) was observed from samples obtained in Spain (P =&#x2009;0.002). Geography showed no significant effects on community composition via an ANOSIM using Bray-Curtis dissimilarities (R&#x2009;=&#x2009;0.03, P =&#x2009;0.21). Bacterial functional analysis prediction obtained by PICRUSt showed that 5.7% KEGG pathways differed between the Spain and USA samples.<br><br>CONCLUSIONS: The taxonomic assessment alone does not fully capture the microbiome's differences from two different geographical locations. Carbohydrate and amino acid metabolism were enriched in samples from Spain, while samples from the USA had a higher representation of pathways related to nitrogen, propanoate metabolism, and secretion systems.}, }
@article {pmid37208622, year = {2023}, author = {Yuan, T and Xia, Y and Li, B and Yu, W and Rao, T and Ye, Z and Yan, X and Song, B and Li, L and Lin, F and Cheng, F}, title = {Gut microbiota in patients with kidney stones: a systematic review and meta-analysis.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {143}, pmid = {37208622}, issn = {1471-2180}, abstract = {BACKGROUND: Mounting evidence indicates that the gut microbiome (GMB) plays an essential role in kidney stone (KS) formation. In this study, we conducted a systematic review and meta-analysis to compare the composition of gut microbiota in kidney stone patients and healthy individuals, and further understand the role of gut microbiota in nephrolithiasis.<br><br>RESULTS: Six databases were searched to find taxonomy-based comparison studies on the GMB until September 2022. Meta-analyses were performed using RevMan 5.3 to estimate the overall relative abundance of gut microbiota in KS patients and healthy subjects. Eight studies were included with 356 nephrolithiasis patients and 347 healthy subjects. The meta-analysis suggested that KS patients had a higher abundance of Bacteroides (35.11% vs 21.25%, Z&#x2009;=&#x2009;3.56, P&#x2009;=&#x2009;0.0004) and Escherichia_Shigella (4.39% vs 1.78%, Z&#x2009;=&#x2009;3.23, P&#x2009;=&#x2009;0.001), and a lower abundance of Prevotella_9 (8.41% vs 10.65%, Z&#x2009;=&#x2009;4.49, P&#x2009;<&#x2009;0.00001). Qualitative analysis revealed that beta-diversity was different between the two groups (P&#x2009;<&#x2009;0.05); Ten taxa (Bacteroides, Phascolarctobacterium, Faecalibacterium, Flavobacterium, Akkermansia, Lactobacillus, Escherichia coli, Rhodobacter and Gordonia) helped the detection of kidney stones (P&#x2009;<&#x2009;0.05); Genes or protein families of the GMB involved in oxalate degradation, glycan synthesis, and energy metabolism were altered in patients (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: There is a characteristic gut microbiota dysbiosis in kidney stone patients. Individualized therapies like microbial supplementation, probiotic or synbiotic preparations and adjusted diet patterns based on individual gut microbial characteristics of patients may be more effective in preventing stone formation and recurrence.}, }
@article {pmid37208617, year = {2023}, author = {Liao, F and Qian, J and Yang, R and Gu, W and Li, R and Yang, T and Fu, X and Yuan, B and Zhang, Y}, title = {Metagenomics of gut microbiome for migratory seagulls in Kunming city revealed the potential public risk to human health.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {269}, pmid = {37208617}, issn = {1471-2164}, abstract = {BACKGROUND: Seagull as a migratory wild bird has become most popular species in southwest China since 1980s. Previously, we analyzed the gut microbiota and intestinal pathogenic bacteria configuration for this species by using 16S rRNA sequencing and culture methods. To continue in-depth research on the gut microbiome of migratory seagulls, the metagenomics, DNA virome and RNA virome were both investigated for their gut microbial communities of abundance and diversity in this study.<br><br>RESULTS: The metagenomics results showed 99.72% of total species was bacteria, followed by viruses, fungi, archaea and eukaryota. In particular, Shigella sonnei, Escherichia albertii, Klebsiella pneumonia, Salmonella enterica and Shigella flexneri were the top distributed taxa at species level. PCoA, NMDS, and statistics indicated some drug resistant genes, such as adeL, evgS, tetA, PmrF, and evgA accumulated as time went by from November to January of the next year, and most of these genes were antibiotic efflux. DNA virome composition demonstrated that Caudovirales was the most abundance virus, followed by Cirlivirales, Geplafuvirales, Petitvirales and Piccovirales. Most of these phages corresponded to Enterobacteriaceae and Campylobacteriaceae bacterial hosts respectively. Caliciviridae, Coronaviridae and Picornaviridae were the top distributed RNA virome at family level of this migratory animal. Phylogenetic analysis indicated the sequences of contigs of Gammacoronavirus and Deltacoronavirus had highly similarity with some coronavirus references.<br><br>CONCLUSIONS: In general, the characteristics of gut microbiome of migratory seagulls were closely related to human activities, and multiomics still revealed the potential public risk to human health.}, }
@article {pmid37208594, year = {2023}, author = {Limaye, MA and Brubaker, S and Randis, TM and Ratner, AJ}, title = {Vaginal carriage of Haemophilus influenzae in a non-pregnant reproductive-age population.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {141}, pmid = {37208594}, issn = {1471-2180}, abstract = {BACKGROUND: Haemophilus influenzae (Hi) is an emerging cause of early onset neonatal sepsis, but mechanisms of transmission are not well understood. We aimed to determine the prevalence of vaginal carriage of Hi in reproductive age women and to examine behavioral and demographic characteristics associated with its carriage.<br><br>METHODS: We performed a secondary analysis of stored vaginal lavage specimens from a prospective cohort study of nonpregnant reproductive-age women. After extraction of bacterial genomic DNA, samples were tested for the presence of the gene encoding Haemophilus protein d (hpd) by quantitative real-time polymerase chain reaction (PCR) using validated primers and probe. PCR for the V3-V4 region of the 16&#xa0;S rRNA gene (positive control) assessed sample quality. Samples with cycle threshold (CT) value&#x2009;<&#x2009;35 were defined as positive. Sanger sequencing confirmed the presence of hpd. Behavioral and demographic characteristics associated with vaginal carriage of Hi were examined.<br><br>RESULTS: 415 samples were available. 315 (75.9%) had sufficient bacterial DNA and were included. 14 (4.4%) were positive for hpd. There were no demographic or behavioral differences between the women with Hi vaginal carriage and those without. There was no difference in history of bacterial vaginosis, vaginal microbiome community state type, or presence of Group B Streptococcus in women with and without vaginal carriage of Hi.<br><br>CONCLUSION: Hi was present in vaginal lavage specimens of 4.4% of this cohort. Hi presence was unrelated to clinical or demographic characteristics, though the relatively small number of positive samples may have limited power to detect such differences.}, }
@article {pmid37208544, year = {2023}, author = {Lange, O and Proczko-Stepaniak, M and Mika, A}, title = {Short-Chain Fatty Acids-A Product of the Microbiome and Its Participation in Two-Way Communication on the Microbiome-Host Mammal Line.}, journal = {Current obesity reports}, volume = {}, number = {}, pages = {}, pmid = {37208544}, issn = {2162-4968}, abstract = {PURPOSE OF REVIEW: The review aims to describe short-chain fatty acids (SCFAs) as metabolites of bacteria, their complex influence on whole-body metabolism, and alterations in the SCFA profile in obesity and after bariatric surgery (BS).<br><br>RECENT FINDINGS: The fecal profile of SCFAs in obese patients differs from that of lean patients, as well as their gut microbiota composition. In obese patients, a lower diversity of bacteria is observed, as well as higher concentrations of SCFAs in stool samples. Obesity is now considered a global epidemic and bariatric surgery (BS) is an effective treatment for severe obesity. BS affects the structure and functioning of the digestive system, and also alters gut microbiota and the concentration of fecal SCFAs. Generally, after BS, SCFA levels are lower but levels of branched short-chain fatty acids (BSCFAs) are elevated, the effect of which is not fully understood. Moreover, changes in the profile of circulating SCFAs are little known and this is an area for further research. Obesity seems to be inherently associated with changes in the SCFA profile. It is necessary to better understand the impact of BS on microbiota and the metabolome in both feces and blood as only a small percentage of SCFAs are excreted. Further research may allow the development of a personalized therapeutic approach to the BS patient in terms of diet and prebiotic intervention.}, }
@article {pmid37208436, year = {2023}, author = {Winders, TM and Holman, DB and Schmidt, KN and Luecke, SM and Smith, DJ and Neville, BW and Dahlen, CR and Swanson, KC and Amat, S}, title = {Feeding hempseed cake alters the bovine gut, respiratory and reproductive microbiota.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8121}, pmid = {37208436}, issn = {2045-2322}, abstract = {A growing number of studies have investigated the feasibility of utilizing hemp by-products as livestock feedstuffs; however, their impact on livestock microbiomes remains unexplored. Here, we evaluated the effects of feeding hempseed cake on the gastrointestinal, respiratory, and reproductive microbiota in beef heifers. Angus-crossbred heifers (19-months old, initial body weight = 494 ± 10 kg [SE]) were fed a corn-based finishing diet containing 20% hempseed cake as a substitute for 20% corn dried distillers' grains with solubles (DM basis; Control; n = 16/group) for 111 days until slaughter. Ruminal fluid and deep nasopharyngeal swabs (days 0, 7, 42, 70 and 98), and vaginal and uterine swabs (at slaughter) were collected, and the microbiota assessed using 16S rRNA gene sequencing. Diet affected the community structure of the ruminal (d 7-98; 0.06 ≤ R[2] ≤ 0.12; P < 0.05), nasopharyngeal (d 98; R[2] = 0.18; P < 0.001), and vaginal (R[2] = 0.06; P < 0.01) microbiota. Heifers fed hempseed cake had increased microbial diversity in the rumen, reduced microbial richness in the vagina, and greater microbial diversity and richness in the uterus. In addition to the distinct microbial communities in the rumen, nasopharynx, vagina and uterus, we identified 28 core taxa that were shared (≥ 60% of all samples) across these sampling locations. Feeding hempseed cake appeared to alter the bovine gut, respiratory and reproductive microbiota. Our results suggest that future research aiming to evaluate the use of hemp by-products in livestock diet should consider their impact on animal microbiome and microbiome mediated animal health and reproductive efficiency. Our findings also highlight the need for research evaluating the impact of hemp-associated food and personal care products on the human microbiome.}, }
@article {pmid37208257, year = {2023}, author = {Wang, Q and Wu, S and Ye, X and Tan, S and Huang, F and Su, G and Kijlstra, A and Yang, P}, title = {Gut microbial signatures and their functions in Behcet's uveitis and Vogt-Koyanagi-Harada disease.}, journal = {Journal of autoimmunity}, volume = {}, number = {}, pages = {103055}, doi = {10.1016/j.jaut.2023.103055}, pmid = {37208257}, issn = {1095-9157}, abstract = {BACKGROUND: A number of public metagenomic studies reveal an association between the gut microbiome and various immune-mediated diseases including Behcet's uveitis (BU) and Vogt-Koyanagi-Harada disease (VKH). Integrated-analysis and subsequent validation of these results could be a potentially powerful way to understand the microbial signatures and their functions in these two uveitis entities.<br><br>METHODS: We integrated the sequencing data of our previous metagenomic studies on two major uveitis entities, BU and VKH as well as four other publicly available immune-mediated diseases datasets, including Ankylosing Spondylitis (AS), Rheumatoid Arthritis (RA), Crohn's disease (CD) and Ulcerative Colitis (UC). Alpha-diversity and beta-diversity analysis were used to compare the gut microbiome signatures between both uveitis entities and other immune-mediated diseases and healthy controls. Amino acid homology between microbial proteins and a uveitogenic peptide of the interphotoreceptor retinoid-binding protein (IRBP)161-180 was investigated using a similarity search in the NCBI protein BLAST program (BLASTP). Enzyme-linked Immunosorbent Assay (ELISA) was performed to evaluate the cross-reactive responses of experimental autoimmune uveitis (EAU)-derived lymphocytes and BU patients-derived peripheral blood mononuclear cells (PBMCs) against homologous peptides. The area under the curve (AUC) analysis was used to test the sensitivity and specificity of gut microbial biomarkers.<br><br>RESULTS: Depleted Dorea, Blautia, Coprococcus, Erysipelotrichaceae and Lachnospiraceae as well as enriched Bilophila and Stenotrophomonas were identified in BU patients. An enriched Alistipes along with a lower level of Dorea were observed in VKH patients. A peptide antigen (SteTDR) encoded by BU specifically enriched Stenotrophomonas was identified to share homology with IRBP161-180. In vitro experiments showed that lymphocytes from EAU or PBMCs from BU patients reacted to this peptide antigen as shown by the production of IFN-&#x3b3; and IL-17. Addition of the SteTDR peptide to the classical IRBP immunization protocol exacerbated EAU severity. Gut microbial marker profiles consisted of 24 species and 32 species respectively differentiated BU and VKH from each other as well as from the other four immune-mediated diseases and healthy controls. Protein annotation identified 148 and 119 specific microbial proteins associated with BU and VKH, respectively. For metabolic function analysis, 108 and 178 metabolic pathways were shown to be associated with BU and VKH, respectively.<br><br>CONCLUSIONS: Our study revealed specific gut microbial signatures and their potentially functional roles in BU and VKH pathogenesis that differ significantly from other immune-mediated diseases as well as healthy controls.}, }
@article {pmid37208218, year = {2023}, author = {Sola-Leyva, A and Pérez-Prieto, I and Molina, NM and Vargas, E and Ruiz-Durán, S and Leonés-Baños, I and Canha-Gouveia, A and Altmäe, S}, title = {Microbial composition across body sites in polycystic ovary syndrome: a systematic review and meta-analysis.}, journal = {Reproductive biomedicine online}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.rbmo.2023.03.016}, pmid = {37208218}, issn = {1472-6491}, abstract = {Polycystic ovary syndrome (PCOS) is an endocrine disorder affecting reproductive-aged women, but the cause remains unclear. Recent evidence has linked microbial composition with PCOS; however, the results are inconsistent. The aim of this systematic review was to gather current knowledge of the microbes across body sites (oral cavity, blood, vagina/cervix, gut) in women with PCOS, and meta-analyse the microbial diversity in PCOS. For this purpose, a systematic search using PubMed, Web of Science, Cochrane and Scopus was carried out. After selection, 34 studies met the inclusion criteria. Most of the studies associated changes in the microbiome with PCOS, whereas heterogeneity of the studies in terms of ethnicity, body mass index (BMI) and methodology, among other confounders, made it difficult to corroborate this relationship. In fact, 19 out of 34 of the studies were categorised as having high risk of bias when the quality assessment was conducted. Our meta-analysis on the gut microbiome of 14 studies demonstrated that women with PCOS possess significantly lower microbial alpha diversity compared with controls (SMD = -0.204; 95% CI -0.360 to -0.048; P = 0.010; I[2] = 5.508, by Shannon Index), which may contribute to the development of PCOS. Nevertheless, future studies should specifically overcome the shortcomings of the current studies by through well planned and conducted studies with larger sample sizes, proper negative and positive controls and adequate case-control matching.}, }
@article {pmid37207856, year = {2023}, author = {Kyser, AJ and Mahmoud, MY and Herold, SE and Lewis, WG and Lewis, AL and Steinbach-Rankins, JM and Frieboes, HB}, title = {Formulation and Characterization of Pressure-Assisted Microsyringe 3D-Printed Scaffolds for Controlled Intravaginal Antibiotic Release.}, journal = {International journal of pharmaceutics}, volume = {}, number = {}, pages = {123054}, doi = {10.1016/j.ijpharm.2023.123054}, pmid = {37207856}, issn = {1873-3476}, abstract = {Bacterial vaginosis (BV) is a highly recurrent vaginal condition linked with many health complications. Topical antibiotic treatments for BV are challenged with drug solubility in vaginal fluid, lack of convenience and user adherence to daily treatment protocols, among other factors. 3D-printed scaffolds can provide sustained antibiotic delivery to the female reproductive tract (FRT). Silicone vehicles have been shown to provide structural stability, flexibility, and biocompatibility, with favorable drug release kinetics. This study formulates and characterizes novel metronidazole-containing 3D-printed silicone scaffolds for eventual application to the FRT. Scaffolds were evaluated for degradation, swelling, compression, and metronidazole release in simulated vaginal fluid (SVF). Scaffolds retained high structural integrity and sustained release. Minimal mass loss (<6%) and swelling (<2%) were observed after 14 days in SVF, relative to initial post-cure measurements. Scaffolds cured for 24 hr (50°C) demonstrated elastic behavior under 20% compression and 4.0 N load. Scaffolds cured for 4 hr (50°C), followed by 72 hr (4°C), demonstrated the highest, sustained, metronidazole release (4.0 and 27.0 µg/mg) after 24 hr and 14 days, respectively. Based upon daily release profiles, it was observed that the 24 hr timepoint had the greatest metronidazole release of 4.08 μg/mg for scaffolds cured at 4 hr at 50°C followed by 72 hr at 4°C. For all curing conditions, release of metronidazole after 1 and 7 days showed >4.0-log reduction in Gardnerella concentration. Negligible cytotoxicity was observed in treated keratinocytes comparable to untreated cells, This study shows that pressure-assisted microsyringe 3D-printed silicone scaffolds may provide a versatile vehicle for sustained metronidazole delivery to the FRT.}, }
@article {pmid37207855, year = {2023}, author = {Maeng, LY and Beumer, A}, title = {Never fear, the gut bacteria are here: Estrogen and gut microbiome-brain axis interactions in fear extinction.}, journal = {International journal of psychophysiology : official journal of the International Organization of Psychophysiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijpsycho.2023.05.350}, pmid = {37207855}, issn = {1872-7697}, abstract = {Sex differences in the prevalence, symptomatology, severity, and other aspects of various neuropsychiatric diseases have been consistently reported. Stress and fear-related psychopathologies, such as anxiety disorders, depression, and post-traumatic stress disorder, are more prevalent in women. Investigations of the mechanisms underlying this sex disparity have described the influence of gonadal hormones in both humans and animal models. However, gut microbial communities are also likely to play a role, as these communities differ between the sexes, are involved in a bidirectional cycling of sex hormones and their metabolites, and are associated with changes in fear-related psychopathologies when gut microbiota are altered or removed. Here, we focus our review on: (1) the role of gut microbiota-brain connections in stress- and fear-based psychiatric disorders, (2) gut microbiota interactions with sex hormones with a particular focus on estrogen, and (3) investigations of these estrogen-gut microbiome interactions in fear extinction, a laboratory model of exposure therapy, to elucidate potential targets for psychiatric treatment. Finally, we call for more mechanistic research using female rodent models and humans.}, }
@article {pmid37207833, year = {2023}, author = {Schmidt-Jeffris, RA}, title = {Non-target pesticide impacts on pest natural enemies: Progress and gaps in current knowledge.}, journal = {Current opinion in insect science}, volume = {}, number = {}, pages = {101056}, doi = {10.1016/j.cois.2023.101056}, pmid = {37207833}, issn = {2214-5753}, abstract = {Avoiding pesticide non-target effects on natural enemies is a cornerstone of conservation biological control. Recent advances in this field have included increased examination of nuanced sublethal effects, including microbiome changes. There is an interest in lifetable-based approaches, while also simplifying results to reduce the amount of information a grower needs to interpret to make a judicious application decision. Newer pesticides are showing promise for selectivity to both natural enemies and humans. Major research gaps still remain, with few published studies on ground-dwelling natural enemies, herbicides, adjuvants, or pesticide mixes. Translating the results of laboratory assays to field-level effects remains a major challenge. Field studies examining entire management programs and meta-analyses of laboratory studies may begin to address this issue.}, }
@article {pmid37207756, year = {2023}, author = {Zang, Y and Du, C and Xin, R and Cao, Y and Zuo, F}, title = {Anti-diabetic effect of modified 'Guanximiyou' pummelo peel pectin on type 2 diabetic mice via gut microbiota.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {124865}, doi = {10.1016/j.ijbiomac.2023.124865}, pmid = {37207756}, issn = {1879-0003}, abstract = {This study aimed to investigate the mechanisms of nature and modified 'Guanximiyou' pummelo peel pectin (GGP and MGGP) in alleviating T2DM through in vitro and in vivo. After modification, pectin was transformed from high methoxy pectin (HMP) to low methoxy pectin (LMP), and the content of galacturonic acid was increased. These made MGGP have stronger antioxidant capacity and better inhibition effect on corn starch digestion in vitro. In vivo experiments have shown that both GGP and MGGP inhibited the development of diabetes after 4 weeks of ingestion. However, MGGP can more effectively reduce blood glucose and regulate lipid metabolism, and has significant antioxidant capacity and the ability to promote SCFAs secretion. In addition, 16S rRNA analysis showed that MGGP changed the composition of intestinal microbiota in diabetic mice, decreased the abundance of Proteobacteria, and increased the relative abundance of Akkermansia, Lactobacillus, Oscillospirales and Ruminococcaceae. The phenotypes of the gut microbiome also changed accordingly, indicating that MGGP can inhibit the growth of pathogenic bacteria, alleviate intestinal functional metabolic disorders and reverse the potential risk of related complications. Altogether, our findings demonstrate that MGGP, as a dietary polysaccharide, may inhibit the development of diabetes by reversing the imbalance of gut microbiota.}, }
@article {pmid37207736, year = {2023}, author = {Ren, H and Wang, G and Ding, W and Li, H and Shen, X and Shen, D and Jiang, X and Qadeer, A}, title = {Response of dissolved organic matter (DOM) and microbial community to submerged macrophytes restoration in lakes: A review.}, journal = {Environmental research}, volume = {}, number = {}, pages = {116185}, doi = {10.1016/j.envres.2023.116185}, pmid = {37207736}, issn = {1096-0953}, abstract = {Microorganisms play a crucial role in the biogeochemical processes of Dissolved Organic Matter (DOM), and the properties of DOM also significantly influence changes in microbial community characteristics. This interdependent relationship is vital for the flow of matter and energy within aquatic ecosystems. The presence, growth state, and community characteristics of submerged macrophytes determine the susceptibility of lakes to eutrophication, and restoring a healthy submerged macrophyte community is an effective way to address this issue. However, the transition from eutrophic lakes dominated by planktic algae to medium or low trophic lakes dominated by submerged macrophytes involves significant changes. Changes in aquatic vegetation have greatly affected the source, composition, and bioavailability of DOM. The adsorption and fixation functions of submerged macrophytes determine the migration and storage of DOM and other substances from water to sediment. Submerged macrophytes regulate the characteristics and distribution of microbial communities by controlling the distribution of carbon sources and nutrients in the lake. They further affect the characteristics of the microbial community in the lake environment through their unique epiphytic microorganisms. The unique process of submerged macrophyte recession or restoration can alter the DOM-microbial interaction pattern in lakes through its dual effects on DOM and microbial commu-----nities, ultimately changing the stability of carbon and mineralization pathways in lakes, such as the release of methane and other greenhouse gases. This review provides a fresh perspective on the dynamic changes of DOM and the role of the microbiome in the future of lake ecosystems.}, }
@article {pmid37207649, year = {2023}, author = {Liang, W and Yang, Y and Gong, S and Wei, M and Ma, Y and Feng, R and Gao, J and Liu, X and Tu, F and Ma, W and Yi, X and Liang, Z and Wang, F and Wang, L and Chen, D and Shu, W and Miller, BE and Tal-Singer, R and Donaldson, GC and Wedzicha, JA and Singh, D and Wilkinson, TMA and Brightling, CE and Chen, R and Zhong, N and Wang, Z}, title = {Airway dysbiosis accelerates lung function decline in chronic obstructive pulmonary disease.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2023.04.018}, pmid = {37207649}, issn = {1934-6069}, abstract = {Progressive lung function decline is a hallmark of chronic obstructive pulmonary disease (COPD). Airway dysbiosis occurs in COPD, but whether it contributes to disease progression remains unknown. Here, we show, through a longitudinal analysis of two cohorts involving four UK centers, that baseline airway dysbiosis in COPD patients, characterized by the enrichment of opportunistic pathogenic taxa, associates with a rapid forced expiratory volume in 1 s (FEV1) decline over 2 years. Dysbiosis associates with exacerbation-related FEV1 fall and sudden FEV1 fall at stability, contributing to long-term FEV1 decline. A third cohort in China further validates the microbiota-FEV1-decline association. Human multi-omics and murine studies show that airway Staphylococcus aureus colonization promotes lung function decline through homocysteine, which elicits a neutrophil apoptosis-to-NETosis shift via the AKT1-S100A8/A9 axis. S. aureus depletion via bacteriophages restores lung function in emphysema mice, providing a fresh approach to slow COPD progression by targeting the airway microbiome.}, }
@article {pmid37207356, year = {2023}, author = {Jones, HJ and Bourke, CD and Swann, JR and Robertson, RC}, title = {Malnourished Microbes: Host-Microbiome Interactions in Child Undernutrition.}, journal = {Annual review of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-nutr-061121-091234}, pmid = {37207356}, issn = {1545-4312}, abstract = {Childhood undernutrition is a major global health burden that is only partially resolved by nutritional interventions. Both chronic and acute forms of child undernutrition are characterized by derangements in multiple biological systems including metabolism, immunity, and endocrine systems. A growing body of evidence supports a role of the gut microbiome in mediating these pathways influencing early life growth. Observational studies report alterations in the gut microbiome of undernourished children, while preclinical studies suggest that this can trigger intestinal enteropathy, alter host metabolism, and disrupt immune-mediated resistance against enteropathogens, each of which contribute to poor early life growth. Here, we compile evidence from preclinical and clinical studies and describe the emerging pathophysiological pathways by which the early life gut microbiome influences host metabolism, immunity, intestinal function, endocrine regulation, and other pathways contributing to child undernutrition. We discuss emerging microbiome-directed therapies and consider future research directions to identify and target microbiome-sensitive pathways in child undernutrition. Expected final online publication date for the Annual Review of Nutrition, Volume 43 is August 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, }
@article {pmid37207228, year = {2023}, author = {Zhang, Z and Liu, Z and Lv, A and Fan, C}, title = {How Toll-like receptors influence Parkinson's disease in the microbiome-gut-brain axis.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1154626}, doi = {10.3389/fimmu.2023.1154626}, pmid = {37207228}, issn = {1664-3224}, abstract = {Recently, a large number of experimenters have found that the pathogenesis of Parkinson's disease may be related to the gut microbiome and proposed the microbiome-gut-brain axis. Studies have shown that Toll-like receptors, especially Toll-like receptor 2 (TLR2) and Toll-like receptor 4 (TLR4), are key mediators of gut homeostasis. In addition to their established role in innate immunity throughout the body, research is increasingly showing that the Toll-like receptor 2 and Toll-like receptor 4 signaling pathways shape the development and function of the gut and enteric nervous system. Notably, Toll-like receptor 2 and Toll-like receptor 4 are dysregulated in Parkinson's disease patients and may therefore be identified as the core of early gut dysfunction in Parkinson's disease. To better understand the contribution of Toll-like receptor 2 and Toll-like receptor 4 dysfunction in the gut to early α-synuclein aggregation, we discussed the structural function of Toll-like receptor 2 and Toll-like receptor 4 and signal transduction of Toll-like receptor 2 and Toll-like receptor 4 in Parkinson's disease by reviewing clinical, animal models, and in vitro studies. We also present a conceptual model of the pathogenesis of Parkinson's disease, in which microbial dysbiosis alters the gut barrier as well as the Toll-like receptor 2 and Toll-like receptor 4 signaling pathways, ultimately leading to a positive feedback loop for chronic gut dysfunction, promoting α-synuclein aggregation in the gut and vagus nerve.}, }
@article {pmid37207189, year = {2023}, author = {Gamsjäger, L and Cirone, KM and Schluessel, S and Campsall, M and Herik, A and Lahiri, P and Young, D and Dufour, A and Sapountzis, P and Otani, S and Gomez, DE and Windeyer, MC and Cobo, ER}, title = {Host innate immune responses and microbiome profile of neonatal calves challenged with Cryptosporidium parvum and the effect of bovine colostrum supplementation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1165312}, doi = {10.3389/fcimb.2023.1165312}, pmid = {37207189}, issn = {2235-2988}, abstract = {INTRODUCTION: Calves are highly susceptible to gastrointestinal infection with Cryptosporidium parvum (C. parvum), which can result in watery diarrhea and eventually death or impaired development. With little to no effective therapeutics, understanding the host's microbiota and pathogen interaction at the mucosal immune system has been critical to identify and test novel control strategies.<br><br>METHODS: Herein, we used an experimental model of C. parvum challenge in neonatal calves to describe the clinical signs and histological and proteomic profiling of the mucosal innate immunity and microbiota shifts by metagenomics in the ileum and colon during cryptosporidiosis. Also, we investigated the impact of supplemental colostrum feeding on C. parvum infection.<br><br>RESULTS: We showed that C. parvum challenged calves experienced clinical signs including pyrexia and diarrhea 5 days post challenge. These calves showed ulcerative neutrophil ileitis with a proteomic signature driven by inflammatory effectors, including reactive oxygen species and myeloperoxidases. Colitis was also noticed with an aggravated mucin barrier depletion and incompletely filled goblet cells. The C. parvum challenged calves also displayed a pronounced dysbiosis with a high prevalence of Clostridium species (spp.) and number of exotoxins, adherence factors, and secretion systems related to Clostridium spp. and other enteropathogens, including Campylobacter spp., Escherichia sp., Shigella spp., and Listeria spp. Daily supplementation with a high-quality bovine colostrum product mitigated some of the clinical signs and modulated the gut immune response and concomitant microbiota to a pattern more similar to that of healthy unchallenged calves.<br><br>DISCUSSION: C. parvum infection in neonatal calves provoked severe diarrheic neutrophilic enterocolitis, perhaps augmented due to the lack of fully developed innate gut defenses. Colostrum supplementation showed limited effect mitigating diarrhea but demonstrated some clinical alleviation and specific modulatory influence on host gut immune responses and concomitant microbiota.}, }
@article {pmid37207186, year = {2023}, author = {Hao, SR and Zhou, YY and Zhang, X and Jiang, HY}, title = {Gut microbiome profiles may be related to atypical antipsychotic associated overweight in Asian children with psychiatric disorder: a preliminary study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1124846}, doi = {10.3389/fcimb.2023.1124846}, pmid = {37207186}, issn = {2235-2988}, abstract = {OBJECTIVE: Atypical antipsychotics (APs) modify the gut microbiome, and weight gain in response to AP could be mediated by the gut microbiome. Thus, the present study aimed to explore the changes in the gut bacterial microbiome in AP-exposed children with obesity.<br><br>METHODS: To rule out the confounder of AP indication, the gut bacterial microbiome was compared between healthy controls (Con) and AP-exposed individuals with overweight (APO) or normal weight (APN). Fifty-seven AP-treated outpatients (21 APO and 36 APN) and 25 Con were included in this cross-sectional microbiota study.<br><br>RESULTS: AP users, regardless of body mass index, exhibited decreased microbial richness and diversity and a distinct metagenomic composition compared to the Con. Although no differences in the microbiota structure were observed between APO and APN groups, the APO group was characterised by a higher abundance of Megamonas and Lachnospira. Additionally, the differences in the microbial functions were observed between APO and APN groups.<br><br>CONCLUSIONS: The gut bacterial microbiota of APO children revealed taxonomic and functional differences compared to Con and APN. Further studies are needed to verify these findings and to explore the temporal and causal relationships between these variables.}, }
@article {pmid37207140, year = {2023}, author = {Gandini, A and Puglisi, S and Pirrone, C and Martelli, V and Catalano, F and Nardin, S and Seeber, A and Puccini, A and Sciallero, S}, title = {The role of immunotherapy in microsatellites stable metastatic colorectal cancer: state of the art and future perspectives.}, journal = {Frontiers in oncology}, volume = {13}, number = {}, pages = {1161048}, doi = {10.3389/fonc.2023.1161048}, pmid = {37207140}, issn = {2234-943X}, abstract = {Colorectal cancer (CRC) is the third leading cause of cancer-related deaths worldwide, despite several advances has been achieved in last decades. Few prognostic and predictive biomarkers guide therapeutic choice in metastatic CRC (mCRC), among which DNA mismatch repair deficiency and/or microsatellite instability (dMMR/MSI) holds a crucial role. Tumors characterized by dMMR/MSI benefit from immune checkpoint inhibitors. However, most of the mCRC patients (around 95%) are microsatellite stable (MSS), thereby intrinsically resistant to immunotherapy. This represents a clear unmet need for more effective treatments in this population of patients. In this review, we aim to analyze immune-resistance mechanisms and therapeutic strategies to overcome them, such as combinations of immunotherapy and chemotherapy, radiotherapy or target therapies specifically in MSS mCRC. We also explored both available and potential biomarkers that may better select MSS mCRC patients for immunotherapy. Lastly, we provide a brief overview on future perspectives in this field, such as the gut microbiome and its potential role as immunomodulator.}, }
@article {pmid37206972, year = {2023}, author = {Stefani, F and Beguin, J and Paré, D and Morency, MJ and Martineau, C and Fortin, JA and Thiffault, N and Séguin, A}, title = {Does wood mulch trigger microbially mediated positive plant-soil feedback in degraded boreal forest sites? A post hoc study.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1122445}, doi = {10.3389/fpls.2023.1122445}, pmid = {37206972}, issn = {1664-462X}, abstract = {INTRODUCTION: Reforestation of degraded lands in the boreal forest is challenging and depends on the direction and strength of the plant-soil feedback (PSF).<br><br>METHODS: Using a gradient in tree productivity (null, low and high) from a long-term, spatially replicated reforestation experiment of borrow pits in the boreal forest, we investigated the interplay between microbial communities and soil and tree nutrient stocks and concentrations in relation to a positive PSF induced by wood mulch amendment.<br><br>RESULTS: Three levels of mulch amendment underlie the observed gradient in tree productivity, and plots that had been amended with a continuous layer of mulch 17 years earlier showed a positive PSF with trees up to 6 m tall, a closed canopy, and a developing humus layer. The average taxonomic and functional composition of the bacterial and fungal communities differed markedly betweenlow- and high-productivity plots. Trees in high-productivity plots recruited a specialized soil microbiome that was more efficient at nutrient mobilization and acquisition. These plots showed increases in carbon (C), calcium (Ca), nitrogen (N), potassium (K), and phosphorus (P) stocks and as well as bacterial and fungal biomass. The soil microbiome was dominated by taxa from the fungal genus Cortinarius and the bacterial family Chitinophagaceae, and a complex microbial network with higher connectivity and more keystone species supported tree productivity in reforested plots compared to unproductive plots.<br><br>DISCUSSION: Therefore, mulching of plots resulted in a microbially mediated PSF that enhances mineral weathering and non-symbiotic N fixation, and in turn helps transform unproductive plots into productive plots to ensure rapid restoration of the forest ecosystem in a harsh boreal environment.}, }
@article {pmid37206897, year = {2023}, author = {Kyritsi, M and Tsiolas, G and Michailidou, S and Koukaras, K and Argiriou, A}, title = {Genomic and 16S metabarcoding data of Holothuria tubulosa Gmelin, 1791.}, journal = {Data in brief}, volume = {48}, number = {}, pages = {109171}, doi = {10.1016/j.dib.2023.109171}, pmid = {37206897}, issn = {2352-3409}, abstract = {Holothuria tubulosa Gmelin, 1791 is an edible sea cucumber species widespread in the Mediterranean Sea with ecological and increasing economic importance. Genome data of holothurian species is limited and the availability of genomic data resources is crucial in understanding their biology and adaptability mechanisms. This dataset presents the raw genome sequence data of H. tubulosa sequenced on an Illumina NextSeq 2000 platform. Genome size estimation was performed based on k-mer frequency approach. Additionally, the bacterial microbiome in the stomach and intestine of H. tubulosa collected from the Strymonian Gulf (North Aegean Sea, Greece) through 16S rRNA amplicon metabarcoding sequencing is reported. Sequencing was performed on an Illumina MiSeq platform. Analysis was conducted using the QIIME2 software package, the DADA2 algorithm and a trained classifier for taxonomy assignment. The datasets presented in this work serve as valuable resources for a comprehensive investigation of H. tubulosa at the genome level and for comparative genomics and echinoderms gut microbial studies.}, }
@article {pmid37206761, year = {2023}, author = {Goulioumis, AK and Kourelis, K and Gkorpa, M and Danielides, V}, title = {Pathogenesis of Nasal Polyposis: Current Trends.}, journal = {Indian journal of otolaryngology and head and neck surgery : official publication of the Association of Otolaryngologists of India}, volume = {75}, number = {Suppl 1}, pages = {733-741}, doi = {10.1007/s12070-022-03247-2}, pmid = {37206761}, issn = {2231-3796}, abstract = {Chronic Rhinosinusitis (CRS) is characterized by edema of the sub-epithelial layers, but, only specific types of CRS are developing polyps. Nasal polyposis may develop under different pathogenetic mechanisms rendering the typical macroscopic classification of CRS, with or without nasal polyps, rather deficient. Currently, we approach nasal polyposis, in terms of diagnosis and treatment, according to its endotype, which means that we focus on the specific cells and cytokines that are participating in its pathogenesis. It appears that the molecular procedures that contribute to polyp formation, initiating with a Th-2 response of the adaptive immune system, are local phenomena occurring in the sub-epithelial layers of the mucosa. Several hypotheses are trying to approach the etiology that drives the immune response towards Th-2 type. Extrinsic factors, like fungi, Staphylococcus superantigens, biofilms, and altered microbiome can contribute to a modified and intense local reaction of the immune system. Some hypotheses based on intrinsic factors like the elimination of Treg lymphocytes, low local vitamin-D levels, high levels of leukotrienes, epithelial to mesenchymal transition (EMT) induced by hypoxia, and altered levels of NO, add pieces to the puzzle of the pathogenesis of nasal polyposis. Currently, the most complete theory is that of epithelial immune barrier dysfunction. Intrinsic and extrinsic conditions can damage the epithelial barrier rendering sub-epithelial layers more vulnerable to invasion by pathogens that trigger a Th-2 response of the adaptive immune system. Th2 cytokines, subsequently, induce the accumulation of eosinophils and IgE together with the remodeling of the stroma in the sub-epithelial layers leading, eventually, to the formation of nasal polyps.}, }
@article {pmid37206729, year = {2023}, author = {Sarkar, S and Routhray, S and Ramadass, B and Parida, PK}, title = {A Review on the Nasal Microbiome and Various Disease Conditions for Newer Approaches to Treatments.}, journal = {Indian journal of otolaryngology and head and neck surgery : official publication of the Association of Otolaryngologists of India}, volume = {75}, number = {Suppl 1}, pages = {755-763}, doi = {10.1007/s12070-022-03205-y}, pmid = {37206729}, issn = {2231-3796}, abstract = {Introduction: Commensal bacteria have always played a significant role in the maintenance of health and disease but are being unravelled only recently. Studies suggest that the nasal microbiome has a significant role in the development of various disease conditions. Search engines were used for searching articles having a nasal microbiome and disease correlation. In olfactory dysfunction, dysbiosis of the microbiome may have a significant role to play in the pathogenesis. The nasal microbiome influences the phenotype of CRS and is also capable of modulating the immune response and plays a role in polyp formation. Microbiome dysbiosis has a pivotal role in the development of Allergic Rhinitis; but, yet known how is this role played. The nasal microbiome has a close association with the severity and phenotype of asthma. They contribute significantly to the onset, severity, and development of asthma. The nasal microbiome has a significant impact on the immunity and protection of its host. The nasal microbiome has been a stimulus in the development of Otitis Media and its manifestations. Studies suggest that the resident nasal microbiome is responsible for the initiation of neurodegenerative diseases like Parkinson's Disease.Materials and Methods: Literature search from PubMed, Medline, and Google with the Mesh terms: nasal microbiome AND diseases. Conclusion: With increasing evidence on the role of the nasal microbiome on various diseases, it would be interesting to see how this microbiome can be modulated by pro/pre/post biotics to prevent a disease or the severity of illness.}, }
@article {pmid37206666, year = {2023}, author = {Goodkin, K and Evering, TH and Anderson, AM and Ragin, A and Monaco, CL and Gavegnano, C and Avery, RJ and Rourke, SB and Cysique, LA and Brew, BJ}, title = {The comorbidity of depression and neurocognitive disorder in persons with HIV infection: call for investigation and treatment.}, journal = {Frontiers in cellular neuroscience}, volume = {17}, number = {}, pages = {1130938}, doi = {10.3389/fncel.2023.1130938}, pmid = {37206666}, issn = {1662-5102}, abstract = {Depression and neurocognitive disorder continue to be the major neuropsychiatric disorders affecting persons with HIV (PWH). The prevalence of major depressive disorder is two to fourfold higher among PWH than the general population (∼6.7%). Prevalence estimates of neurocognitive disorder among PWH range from 25 to over 47% - depending upon the definition used (which is currently evolving), the size of the test battery employed, and the demographic and HIV disease characteristics of the participants included, such as age range and sex distribution. Both major depressive disorder and neurocognitive disorder also result in substantial morbidity and premature mortality. However, though anticipated to be relatively common, the comorbidity of these two disorders in PWH has not been formally studied. This is partly due to the clinical overlap of the neurocognitive symptoms of these two disorders. Both also share neurobehavioral aspects - particularly apathy - as well as an increased risk for non-adherence to antiretroviral therapy. Shared pathophysiological mechanisms potentially explain these intersecting phenotypes, including neuroinflammatory, vascular, and microbiomic, as well as neuroendocrine/neurotransmitter dynamic mechanisms. Treatment of either disorder affects the other with respect to symptom reduction as well as medication toxicity. We present a unified model for the comorbidity based upon deficits in dopaminergic transmission that occur in both major depressive disorder and HIV-associated neurocognitive disorder. Specific treatments for the comorbidity that decrease neuroinflammation and/or restore associated deficits in dopaminergic transmission may be indicated and merit study.}, }
@article {pmid37206364, year = {2023}, author = {Proszkowiec-Weglarz, M and Oakley, B and Ellestad, LE and Javed, S}, title = {Editorial: Avian microbiome: from embryonic development to adulthood.}, journal = {Frontiers in physiology}, volume = {14}, number = {}, pages = {1211911}, doi = {10.3389/fphys.2023.1211911}, pmid = {37206364}, issn = {1664-042X}, }
@article {pmid37206220, year = {2023}, author = {Wang, Y and Chen, WJ and Han, YY and Xu, X and Yang, AX and Wei, J and Hong, DJ and Fang, X and Chen, TT}, title = {Neuroprotective effect of engineered Clostridiumbutyricum-pMTL007-GLP-1 on Parkinson's disease mice models via promoting mitophagy.}, journal = {Bioengineering &amp; translational medicine}, volume = {8}, number = {3}, pages = {e10505}, doi = {10.1002/btm2.10505}, pmid = {37206220}, issn = {2380-6761}, abstract = {Parkinson's disease (PD) is a common neurodegenerative disease with limited treatment and no cure, hence, broadening PD drug spectrum is of great significance. At present, engineered microorganisms are attracting increasing attention. In this study, we constructed an engineered strain of Clostridium butyricum-GLP-1, a C. butyricum (a probiotic) that consistently expresses glucagon-like peptide-1 (GLP-1, a peptide-based hormone with neurological advantage) in anticipation of its use in PD treatment. We further investigated the neuroprotective mechanism of C. butyricum-GLP-1 on PD mice models induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine. The results indicated that C. butyricum-GLP-1 could improve motor dysfunction and ameliorate neuropathological changes by increasing TH expression and reducing the expression of α-syn. Moreover, we confirmed that C. butyricum-GLP-1 improved microbiome imbalance of PD mice by decreasing the relative abundance of Bifidobacterium at the genus level, improved gut integrity, and upregulated the levels of GPR41/43. Surprisingly, we found it could exert its neuroprotective effects via promoting PINK1/Parkin mediated mitophagy and attenuating oxidative stress. Together, our work showed that C. butyricum-GLP-1 improves PD by promoting mitophagy, which provides an alternative therapeutic modality for PD.}, }
@article {pmid37206214, year = {2023}, author = {Kim, J and Hlaing, SP and Lee, J and Kwak, D and Kim, H and Saparbayeva, A and Yoon, IS and Im, E and Jung, Y and Yoo, JW}, title = {pH-sustaining nanostructured hydroxyapatite/alginate composite hydrogel for gastric protection and intestinal release of Lactobacillus rhamnosusGG.}, journal = {Bioengineering &amp; translational medicine}, volume = {8}, number = {3}, pages = {e10527}, doi = {10.1002/btm2.10527}, pmid = {37206214}, issn = {2380-6761}, abstract = {The gut microbiome is closely linked to gastrointestinal health and disease status. Oral administration of known probiotic strains is now considered a promising therapeutic strategy, especially for refractory diseases such as inflammatory bowel disease. In this study, we developed a nanostructured hydroxyapatite/alginate (HAp/Alg) composite hydrogel that protects its encapsulated probiotic Lactobacillus rhamnosus GG (LGG) by neutralizing hydrogen ions that penetrate the hydrogel in a stomach without inhibiting LGG release in an intestine. Surface and transection analyses of the hydrogel revealed characteristic patterns of crystallization and composite-layer formation. TEM revealed the dispersal of the nanosized HAp crystals and encapsulated LGG in the Alg hydrogel networks. The HAp/Alg composite hydrogel maintained its internal microenvironmental pH, thereby enabling the LGG to survive for substantially longer. At intestinal pH, the encapsulated LGG was completely released upon disintegration of the composite hydrogel. In a dextran sulfate sodium-induced colitis mouse model, we then assessed the therapeutic effect of the LGG-encapsulating hydrogel. This achieved intestinal delivery of LGG with minimal loss of enzymatic function and viability, ameliorating colitis by reducing epithelial damage, submucosal edema, inflammatory cell infiltration, and the number of goblet cells. These findings reveal the HAp/Alg composite hydrogel as a promising intestinal-delivery platform for live microorganisms including probiotics and live biotherapeutic products.}, }
@article {pmid37206044, year = {2023}, author = {Cui, Y and Zhang, C and Zhang, X and Yu, X and Ma, Y and Qin, X and Ma, Z}, title = {Integrated serum pharmacochemistry and metabolomics reveal potential effective components and mechanisms of Shengjiang Xiexin decoction in the treatment of Clostridium difficile infection.}, journal = {Heliyon}, volume = {9}, number = {5}, pages = {e15602}, doi = {10.1016/j.heliyon.2023.e15602}, pmid = {37206044}, issn = {2405-8440}, abstract = {Shengjiang Xiexin Decoction (SXD) is a widely recognized formula in Traditional Chinese Medicine (TCM) for treating diarrhea and is commonly used in clinical practice. Clostridium difficile infection (CDI) is a type of antibiotic-associated diarrhea with a rising incidence rate that has severe consequences for humans. Recent clinical applications have found significant efficacy in using SXD as an adjunct to CDI treatment. However, the pharmacodynamic substance basis and therapeutic mechanism of SXD remain unclear. This study aimed to systematically analyze the metabolic mechanisms and key pharmacodynamic components of SXD in CDI mice by combining non-targeted metabolomics of Chinese medicine and serum medicinal chemistry. We established a CDI mouse model to observe the therapeutic effect of SXD on CDI. We investigated the mechanism of action and active substance composition of SXD against CDI by analyzing 16S rDNA gut microbiota, untargeted serum metabolomics, and serum pharmacochemistry. We also constructed a multi-scale, multifactorial network for overall visualization and analysis. Our results showed that SXD significantly reduced fecal toxin levels and attenuated colonic injury in CDI model mice. Additionally, SXD partially restored CDI-induced gut microbiota composition. Non-targeted serum metabolomics studies showed that SXD not only regulated Taurine and hypotaurine metabolism but also metabolic energy and amino acid pathways such as Ascorbate and aldarate metabolism, Glycerolipid metabolism, Pentose and glucuronate interconversions, as well as body and other metabolite production in the host. Through the implementation of network analysis methodologies, we have discerned that Panaxadiol, Methoxylutcolin, Ginsenoside-Rf, Suffruticoside A, and 10 other components serve as critical potential pharmacodynamic substance bases of SXD for CDI. This study reveals the metabolic mechanism and active substance components of SXD for the treatment of CDI mice using phenotypic information, gut microbiome, herbal metabolomics, and serum pharmacochemistry. It provides a theoretical basis for SXD quality control studies.}, }
@article {pmid37205984, year = {2023}, author = {Kepp, O and Zitvogel, L and Kroemer, G}, title = {Prevention and treatment of cancers by tumor antigen-expressing Staphylococcus epidermidis.}, journal = {Oncoimmunology}, volume = {12}, number = {1}, pages = {2212547}, doi = {10.1080/2162402X.2023.2212547}, pmid = {37205984}, issn = {2162-402X}, abstract = {In a recent paper in Science, Chen et al. reported the genetic engineering of S. epidermidis expressing tumor cross-reactive antigens that trigger T cell responses and exhibit anticancer effects after topical administration. Here we discuss direct local effects and indirect systemic effects of exposure to engineered S. epidermidis strains.}, }
@article {pmid37205927, year = {2023}, author = {Eilam, Y and Khattib, H and Pintel, N and Avni, D}, title = {Microalgae-Sustainable Source for Alternative Proteins and Functional Ingredients Promoting Gut and Liver Health.}, journal = {Global challenges (Hoboken, NJ)}, volume = {7}, number = {5}, pages = {2200177}, doi = {10.1002/gch2.202200177}, pmid = {37205927}, issn = {2056-6646}, abstract = {Dietary proteins derived from animal sources, although containing well-balanced profiles of essential amino acids, have considerable environmental and adverse health effects associated with the intake of some animal protein-based products. Consuming foods based on animal proteins carries a higher risk of developing non-communicable diseases such as cancer, heart disease, non-alcoholic fatty liver disease (NAFLD), and inflammatory bowel disease (IBD). Moreover, dietary protein consumption is increasing due to population growth, posing a supply challenge. There is, therefore, growing interest in discovering novel alternative protein sources. In this context, microalgae have been recognized as strategic crops that can provide a sustainable source of protein. Compared to conventional high-protein crops, using microalgal biomass for protein production presents several advantages in food and feed in terms of productivity, sustainability, and nutritional value. Moreover, microalgae positively impact the environment by not exploiting land or causing water pollution. Many studies have revealed the potential of microalgae as an alternative protein source with the added value of positive effects on human health due to their anti-inflammatory, antioxidant, and anti-cancer properties. The main emphasis of this review is on the potential health-promoting applications of microalgae-based proteins, peptides, and bioactive substances for IBD and NAFLD.}, }
@article {pmid37205698, year = {2023}, author = {Jara-Servin, A and Silva, A and Barajas, H and Cruz-Ortega, R and Tinoco-Ojanguren, C and Alcaraz, LD}, title = {Root microbiome diversity and structure of the Sonoran desert buffelgrass (Pennisetum ciliare L.).}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0285978}, doi = {10.1371/journal.pone.0285978}, pmid = {37205698}, issn = {1932-6203}, abstract = {Buffelgrass (Pennisetum ciliare) is an invasive plant introduced into Mexico's Sonoran desert for cattle grazing and has converted large areas of native thorn scrub. One of the invasion mechanisms buffelgrass uses to invade is allelopathy, which consists of the production and secretion of allelochemicals that exert adverse effects on other plants' growth. The plant microbiome also plays a vital role in establishing invasive plants and host growth and development. However, little is known about the buffelgrass root-associated bacteria and the effects of allelochemicals on the microbiome. We used 16S rRNA gene amplicon sequencing to obtain the microbiome of buffelgrass and compare it between samples treated with root exacknudates and aqueous leachates as allelochemical exposure and samples without allelopathic exposure in two different periods. The Shannon diversity values were between H' = 5.1811-5.5709, with 2,164 reported bacterial Amplicon Sequence Variants (ASVs). A total of 24 phyla were found in the buffelgrass microbiome, predominantly Actinobacteria, Proteobacteria, and Acidobacteria. At the genus level, 30 different genera comprised the buffelgrass core microbiome. Our results show that buffelgrass recruits microorganisms capable of thriving under allelochemical conditions and may be able to metabolize them (e.g., Planctomicrobium, Aurantimonas, and Tellurimicrobium). We also found that the community composition of the microbiome changes depending on the developmental state of buffelgrass (p = 0.0366; ANOSIM). These findings provide new insights into the role of the microbiome in the establishment of invasive plant species and offer potential targets for developing strategies to control buffelgrass invasion.}, }
@article {pmid37205696, year = {2023}, author = {Powell, JE and Lau, P and Rangel, J and Arnott, R and De Jong, T and Moran, NA}, title = {The microbiome and gene expression of honey bee workers are affected by a diet containing pollen substitutes.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0286070}, doi = {10.1371/journal.pone.0286070}, pmid = {37205696}, issn = {1932-6203}, abstract = {Pollen is the primary source of dietary protein for honey bees. It also includes complex polysaccharides in its outer coat, which are largely indigestible by bees but can be metabolized by bacterial species within the gut microbiota. During periods of reduced availability of floral pollen, supplemental protein sources are frequently provided to managed honey bee colonies. The crude proteins in these supplemental feeds are typically byproducts from food manufacturing processes and are rarely derived from pollen. Our experiments on the impact of different diets showed that a simplified pollen-free diet formulated to resemble the macronutrient profile of a monofloral pollen source resulted in larger microbial communities with reduced diversity, reduced evenness, and reduced levels of potentially beneficial hive-associated bacteria. Furthermore, the pollen-free diet sharply reduced the expression of genes central to honey bee development. In subsequent experiments, we showed that these shifts in gene expression may be linked to colonization by the gut microbiome. Lastly, we demonstrated that for bees inoculated with a defined gut microbiota, those raised on an artificial diet were less able to suppress infection from a bacterial pathogen than those that were fed natural pollen. Our findings demonstrate that a pollen-free diet significantly impacts the gut microbiota and gene expression of honey bees, indicating the importance of natural pollen as a primary protein source.}, }
@article {pmid37205528, year = {2023}, author = {Alqedari, H and Altabtbaei, K and Espinoza, JL and Bin-Hasan, S and Alghounaim, M and Alawady, A and Altabtabae, A and AlJamaan, S and Devarajan, S and AlShammari, T and Ben Eid, M and Matsuoka, M and Jang, H and Dupont, CL and Freire, M}, title = {Host-Microbiome Associations in Saliva Predict COVID-19 Severity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.05.02.539155}, pmid = {37205528}, abstract = {UNLABELLED: Established evidence indicates that oral microbiota plays a crucial role in modulating host immune responses to viral infection. Following Severe Acute Respiratory Syndrome Coronavirus 2 - SARS-CoV-2 - there are coordinated microbiome and inflammatory responses within the mucosal and systemic compartments that are unknown. The specific roles that the oral microbiota and inflammatory cytokines play in the pathogenesis of COVID-19 are yet to be explored. We evaluated the relationships between the salivary microbiome and host parameters in different groups of COVID-19 severity based on their Oxygen requirement. Saliva and blood samples (n = 80) were collected from COVID-19 and from non-infected individuals. We characterized the oral microbiomes using 16S ribosomal RNA gene sequencing and evaluated saliva and serum cytokines using Luminex multiplex analysis. Alpha diversity of the salivary microbial community was negatively associated with COVID-19 severity. Integrated cytokine evaluations of saliva and serum showed that the oral host response was distinct from the systemic response. The hierarchical classification of COVID-19 status and respiratory severity using multiple modalities separately (i.e., microbiome, salivary cytokines, and systemic cytokines) and simultaneously (i.e., multi-modal perturbation analyses) revealed that the microbiome perturbation analysis was the most informative for predicting COVID-19 status and severity, followed by the multi-modal. Our findings suggest that oral microbiome and salivary cytokines may be predictive of COVID-19 status and severity, whereas atypical local mucosal immune suppression and systemic hyperinflammation provide new cues to understand the pathogenesis in immunologically naïve populations.<br><br>SIGNIFICANCE STATEMENT: The oral mucosa is one of the first sites encountered by bacterial and viral infections, including SARS-CoV-2. It consists of a primary barrier occupied by a commensal oral microbiome. The primary function of this barrier is to modulate immunity and provide protection against invading infection. The occupying commensal microbiome is an essential component that influences the immune system's function and homeostasis. The present study showed that the host oral immune response performs unique functions in response to SARS-CoV-2 when compared to systemic responses during the acute phase. We also demonstrated that there is a link between oral microbiome diversity and COVID-19 severity. Additionally, the salivary microbiome was predictive of not only disease status but also severity.}, }
@article {pmid37205501, year = {2023}, author = {Kicic-Starcevich, E and Hancock, DG and Iosifidis, T and Agudelo-Romero, P and Caparros-Martin, JA and Silva, D and Turkovic, L and Le Souef, PN and Bosco, A and Martino, DJ and Kicic, A and Prescott, SL and Stick, SM}, title = {Airway Epithelium Respiratory Illnesses and Allergy (AERIAL) birth cohort: study protocol.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.04.29.23289314}, pmid = {37205501}, abstract = {INTRODUCTION: Recurrent wheezing disorders including asthma are complex and heterogeneous diseases that affect up to 30% of all children, contributing to a major burden on children, their families, and global healthcare systems. It is now recognized that a dysfunctional airway epithelium plays a central role in the pathogenesis of recurrent wheeze, although the underlying mechanisms are still not fully understood. This prospective birth cohort aims to bridge this knowledge gap by investigating the influence of intrinsic epithelial dysfunction on the risk for developing respiratory disorders and the modulation of this risk by maternal morbidities, in utero exposures, and respiratory exposures in the first year of life.<br><br>METHODS AND ANALYSIS: The Airway Epithelium Respiratory Illnesses and Allergy (AERIAL) study is nested within the ORIGINS Project and will monitor 400 infants from birth to five years. The primary outcome of the AERIAL study will be the identification of epithelial endotypes and exposure variables that influence the development of recurrent wheezing, asthma, and allergic sensitisation. Nasal respiratory epithelium at birth to six weeks, one, three, and five years will be analysed by bulk RNA-seq and DNA methylation sequencing. Maternal morbidities and in utero exposures will be identified on maternal history and their effects measured through transcriptomic and epigenetic analyses of the amnion and newborn epithelium. Exposures within the first year of life will be identified based on infant medical history as well as on background and symptomatic nasal sampling for viral PCR and microbiome analysis. Daily temperatures and symptoms recorded in a study-specific Smartphone App will be used to identify symptomatic respiratory illnesses.<br><br>ETHICS AND DISSEMINATION: Ethical approval has been obtained from Ramsey Health Care HREC WA-SA (#1908). Results will be disseminated through open-access peer-reviewed manuscripts, conference presentations, and through different media channels to consumers, ORIGINS families, and the wider community.}, }
@article {pmid37205444, year = {2023}, author = {Peddada, S and Lin, H}, title = {Multi-group Analysis of Compositions of Microbiomes with Covariate Adjustments and Repeated Measures.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-2778207/v1}, pmid = {37205444}, abstract = {Microbiome differential abundance analysis methods for a pair of groups are well established in the literature. However, many microbiome studies involve multiple groups, sometimes even ordered groups, such as stages of a disease, and require different types of comparisons. Standard pairwise comparisons are not only inefficient in terms of power and false discovery rates, but they may not address the scientific question of interest. In this paper, we propose a general framework for performing a wide range of multi-group analyses with covariate adjustments and repeated measures. We demonstrate the effectiveness of our methodology through two real data sets. The first example explores the effects of aridity on the soil microbiome, and the second example investigates the effects of surgical interventions on the microbiome of IBD patients.}, }
@article {pmid37205434, year = {2023}, author = {Inglis, LK and Roach, MJ and Edwards, RA}, title = {Prophage rates in the human microbiome vary by body site and host health.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.05.04.539508}, pmid = {37205434}, abstract = {Phages integrated into a bacterial genome-called prophages-continuously monitor the health of the host bacteria to determine when to escape the genome, protect their host from other phage infections, and may provide genes that promote bacterial growth. Prophages are essential to almost all microbiomes, including the human microbiome. However, most human microbiome studies focus on bacteria, ignoring free and integrated phages, so we know little about how these prophages affect the human microbiome. We compared the prophages identified in 11,513 bacterial genomes isolated from human body sites to characterise prophage DNA in the human microbiome. Here, we show that prophage DNA comprised an average of 1-5% of each bacterial genome. The prophage content per genome varies with the isolation site on the human body, the health of the human, and whether the disease was symptomatic. The presence of prophages promotes bacterial growth and sculpts the microbiome. However, the disparities caused by prophages vary throughout the body.}, }
@article {pmid37205374, year = {2023}, author = {Salerno, P and Verster, A and Valls, R and Barrack, K and Price, C and Madan, J and O'Toole, GA and Ross, BD}, title = {Persistent delay in maturation of the developing gut microbiota in infants with cystic fibrosis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.05.02.539134}, pmid = {37205374}, abstract = {The healthy human infant gut microbiome undergoes stereotypical changes in taxonomic composition between birth and maturation to an adult-like stable state. During this time, extensive communication between microbiota and the host immune system contributes to health status later in life. Although there are many reported associations between microbiota compositional alterations and disease in adults, less is known about how microbiome development is altered in pediatric diseases. One pediatric disease linked to altered gut microbiota composition is cystic fibrosis (CF), a multi-organ genetic disease involving impaired chloride secretion across epithelia and heightened inflammation both in the gut and at other body sites. Here, we use shotgun metagenomics to profile the strain-level composition and developmental dynamics of the infant fecal microbiota from several CF and non-CF longitudinal cohorts spanning from birth to greater than 36 months of life. We identify a set of keystone species whose prevalence and abundance reproducibly define microbiota development in early life in non-CF infants, but are missing or decreased in relative abundance in infants with CF. The consequences of these CF-specific differences in gut microbiota composition and dynamics are a delayed pattern of microbiota maturation, persistent entrenchment in a transitional developmental phase, and subsequent failure to attain an adult-like stable microbiota. We also detect the increased relative abundance of oral-derived bacteria and higher levels of fungi in CF, features that are associated with decreased gut bacterial density in inflammatory bowel diseases. Our results define key differences in the gut microbiota during ontogeny in CF and suggest the potential for directed therapies to overcome developmental delays in microbiota maturation.}, }
@article {pmid37205350, year = {2023}, author = {Fei, T and Funnell, T and Waters, NR and Raj, SS and Devlin, SM and Dai, A and Miltiadous, O and Shouval, R and Lv, M and Peled, JU and Ponce, DM and Perales, MA and Gönen, M and van den Brink, MRM}, title = {Scalable Log-ratio Lasso Regression Enhances Microbiome Feature Selection for Predictive Models.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.05.02.538599}, pmid = {37205350}, abstract = {Identifying predictive biomarkers of patient outcomes from high-throughput microbiome data is of high interest in contemporary cancer research. We present FLORAL , an open-source computational tool to perform scalable log-ratio lasso regression modeling and microbial feature selection for continuous, binary, time-to-event, and competing risk outcomes. The proposed method adapts the augmented Lagrangian algorithm for a zero-sum constraint optimization problem while enabling a two-stage screening process for extended false-positive control. In extensive simulation studies, FLORAL achieved consistently better false-positive control compared to other lasso-based approaches and better variable selection F 1 score over popular differential abundance approaches. We demonstrate the practical utility of the proposed tool with a real data application on an allogeneic hematopoietic-cell transplantation cohort. The R package is available at https://github.com/vdblab/FLORAL .}, }
@article {pmid37205307, year = {2023}, author = {Kouidhi, S and Zidi, O and Belkhiria, Z and Rais, H and Ayadi, A and Ben Ayed, F and Mosbah, A and Cherif, A and El Gaaied, ABA}, title = {Gut microbiota, an emergent target to shape the efficiency of cancer therapy.}, journal = {Exploration of targeted anti-tumor therapy}, volume = {4}, number = {2}, pages = {240-265}, doi = {10.37349/etat.2023.00132}, pmid = {37205307}, issn = {2692-3114}, abstract = {It is now well-acknowledged that microbiota has a profound influence on both human health and illness. The gut microbiota has recently come to light as a crucial element that influences cancer through a variety of mechanisms. The connections between the microbiome and cancer therapy are further highlighted by a number of preclinical and clinical evidence, suggesting that these complicated interactions may vary by cancer type, treatment, or even by tumor stage. The paradoxical relationship between gut microbiota and cancer therapies is that in some cancers, the gut microbiota may be necessary to maintain therapeutic efficacy, whereas, in other cancers, gut microbiota depletion significantly increases efficacy. Actually, mounting research has shown that the gut microbiota plays a crucial role in regulating the host immune response and boosting the efficacy of anticancer medications like chemotherapy and immunotherapy. Therefore, gut microbiota modulation, which aims to restore gut microbial balance, is a viable technique for cancer prevention and therapy given the expanding understanding of how the gut microbiome regulates treatment response and contributes to carcinogenesis. This review will provide an outline of the gut microbiota's role in health and disease, along with a summary of the most recent research on how it may influence the effectiveness of various anticancer medicines and affect the growth of cancer. This study will next cover the newly developed microbiota-targeting strategies including prebiotics, probiotics, and fecal microbiota transplantation (FMT) to enhance anticancer therapy effectiveness, given its significance.}, }
@article {pmid37205305, year = {2023}, author = {Berg, AK and Grauslund, AC and Nørgaard, K and Thorsen, SU and Zachariae, C and Halling, AS and Jakasa, I and Kezic, S and Svensson, J and Thyssen, JP}, title = {Similar Skin Barrier Function in Persons with Type 1 Diabetes Compared with Healthy Controls.}, journal = {JID innovations : skin science from molecules to population health}, volume = {3}, number = {4}, pages = {100200}, doi = {10.1016/j.xjidi.2023.100200}, pmid = {37205305}, issn = {2667-0267}, abstract = {Contact dermatitis because of use of diabetes devices is frequent in individuals with type 1 diabetes (TD1), especially in the pediatric age group, but the putative role of a constitutional impaired skin barrier in persons with TD1 is unclear. This study examined the skin barrier function by the measurement of natural moisturizing factor and free cytokines collected through skin tape strips, as well as biophysical markers and the skin microbiome, in persons with TD1 than to age- and sex-matched healthy controls. All measurements were done in nonlesional skin. We found that the skin barrier function was similar in children and adolescents with TD1 than to controls but found that the beta-diversity of skin microbiome at the buttock differed between the two groups. We conclude that individuals with TD1 have normal skin barrier function, and that the increased occurrence of contact dermatitis following pump and sensor use is explained by exogenous factors.}, }
@article {pmid37205227, year = {2023}, author = {Karuppannan, AK}, title = {Editorial: Lawsonia intracellularis: a problem well understood is a problem half solved.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1203702}, doi = {10.3389/fvets.2023.1203702}, pmid = {37205227}, issn = {2297-1769}, }
@article {pmid37204436, year = {2023}, author = {Kodila, A and Franko, N and Sollner Dolenc, M}, title = {A review on immunomodulatory effects of BPA analogues.}, journal = {Archives of toxicology}, volume = {}, number = {}, pages = {}, pmid = {37204436}, issn = {1432-0738}, abstract = {Bisphenol A (BPA) is a known endocrine disruptor found in many consumer products that humans come into contact with on a daily basis. Due to increasing concerns about the safety of BPA and the introduction of new legislation restricting its use, industry has responded by adopting new, less studied BPA analogues that have similar polymer-forming properties. Some BPA analogues have already been shown to exhibit effects similar to BPA, for example, contributing to endocrine disruption through agonistic or antagonistic behaviour at various nuclear receptors such as estrogen (ER), androgen (AR), glucocorticoid (GR), aryl hydrocarbon (AhR), and pregnane X receptor (PXR). Since the European Food Safety Authority (EFSA) issued a draft re-evaluation of BPA and drastically reduced the temporary tolerable daily intake (t-TDI) of BPA from 4 mg/kg body weight/day to 0.2 ng/kg body weight/day due to increasing concern about the toxic properties of BPA, including its potential to disrupt immune system processes, we conducted a comprehensive review of the immunomodulatory activity of environmentally abundant BPA analogues. The results of the review suggest that BPA analogues may affect both the innate and acquired immune systems and can contribute to various immune-mediated conditions such as hypersensitivity reactions, allergies, and disruption of the human microbiome.}, }
@article {pmid37204286, year = {2023}, author = {Shankar, A and Das, DJ and Nayar, S and Thomas, S}, title = {Deciphering effect of maternal postpartum antibiotic prophylaxis on infant gut microbiome: a whole metagenomic analysis.}, journal = {Future microbiology}, volume = {}, number = {}, pages = {}, doi = {10.2217/fmb-2022-0200}, pmid = {37204286}, issn = {1746-0921}, abstract = {Aim: To analyze the impact of postpartum antibiotic (Ab) prophylaxis on the infant gut microbiome. Materials &amp; methods: Whole metagenomic analysis was performed on breast milk and infant fecal samples collected from mother-infant pairs who belonged to two groups: an Ab group comprising mothers who had received a single course of Abs in the immediate postpartum period and a non-Ab group comprising mothers who had not received Abs. Results: The characteristic presence of Citrobacter werkmanii, an emerging multidrug-resistant uropathogen, and a higher relative abundance of genes encoding resistance to specific Abs were noted in samples from the Ab group compared with those from the non-Ab group. Conclusion: Policies regarding prophylactic Ab prescription across government and private health sectors in the postpartum period need to be strengthened.}, }
@article {pmid37204063, year = {2023}, author = {Zhao, X and Zhang, T and Zheng, Y and Zhao, Z and Ding, W and Zhang, Z and Zhang, Z and Wang, R and Jiao, M and Liu, L and Yu, S and Wang, X and Huang, R and Wu, Q}, title = {Gut Microbiota from Short-Chain Chlorinated Paraffin-Exposed Mice Promotes Astrocyte Activation by Disrupting the Intestinal Tight Junction via Zonulin Upregulation.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.3c01058}, pmid = {37204063}, issn = {1520-5118}, abstract = {Short-chain chlorinated paraffins (SCCPs) are novel toxicants in food and are reported to possess neurotoxicity. Here, we investigated the mechanism of SCCP-induced astrocyte activation and neuroinflammation. SCCP gavage induced astrocyte activation and neuronal cell death with the changes of gut microbiome and metabolites. Antibiotic cocktail administration to deplete the gut microbiome ameliorated the astrocyte activation and inflammation induced by SCCPs. In fecal microbiota transplantation (FMT) assays, mice that received transplanted gut microbiome from SCCP-treated mice showed increased astrocyte activation and elevated inflammatory response. In addition, SCCP exposure promotes zonulin expression and tight junction injury, and antibiotic cocktail administration inhibited that in the intestinal tract. Increased zonulin and tight junction injury were also observed in SCCPs_FMT mice. The zonulin inhibition protected the tight junction in the intestinal tract from SCCP exposure and suppressed astrocyte activation. In summary, this study proposes a novel possibility for SCCP-induced astrocyte activation and neurotoxicity by the gut microbiome-mediated zonulin expression and tight junction.}, }
@article {pmid37204034, year = {2023}, author = {Liu, M and Liu, H and Li, F and Shen, Y and Zhang, L and Wang, G and Wang, H and Qu, C and Chen, G and Zhao, X and Liu, L and Zhou, J}, title = {Metagenomic Surveillance in Jinan, China Reveals Serum Microbiome and Biochemistry Features in Fever of Unknown Origin (FUO) Patients.}, journal = {Letters in applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/lambio/ovad060}, pmid = {37204034}, issn = {1472-765X}, abstract = {Here we aim to build up a metagenomics-centered surveillance on the infectious microbiome showing in the fever of unknown origin (FUO) patients. We collected venous blood, bronchoalveolar lavage fluid, cerebrospinal fluid, tissue block, sputum, bone marrow biopsy, and purulent liquid samples from 123 patients. Metagenomic sequencing (mNGS) for both DNA and RNA sequences was performed to profile the total pathogenic microbiome in the samples. A large pool of infectious or conditional infectious bacteria were found, belonging to Enterobacteriaceae Staphylococcaceae (10.55%), Burkholderiaceae (10.05%), Comamonadaceae (4.25%). The major viruse families detected from mNGS analysis include Adenoviridae, Anelloviridae, Peribunyaviridae, Flaviviridae and Herpesviridae, showing in 34.96%, 47.37%, 30.89%, 5.69%, 3.25% and 1,63% patients, respectively. Using Ward clustering method, two clusters of patients were organized: high-variety group and low-variety group. The patients in high-variety group demonstrated higher levels of immune cells and inflammatory indicators such as lactate dehydrogenase, aspartate aminotransferase and alanine aminotransferase. The patients in the low-variety group showed higher levels of inflammatory lipids such as 13,14-dihy-15-keto PGE2 (fold > 10, p = 0.021); Tetra-PGDM (fold = 5.29, p = 0.037) and 20-HETE (fold > 10, p = 0.02). The mNGS surveillance system demonstrated remarkable potential in preventing infectious diseases using mNGS data.}, }
@article {pmid37202853, year = {2023}, author = {Velsko, IM and Gallois, S and Stahl, R and Henry, AG and Warinner, C}, title = {High conservation of the dental plaque microbiome across populations with differing subsistence strategies and levels of market integration.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16988}, pmid = {37202853}, issn = {1365-294X}, abstract = {Industrialization-including urbanization, participation in the global food chain and consumption of heavily processed foods-is thought to drive substantial shifts in the human microbiome. While diet strongly influences stool microbiome composition, the influence of diet on the oral microbiome is largely speculative. Multiple ecologically distinct surfaces in the mouth, each harbouring a unique microbial community, pose a challenge to assessing changes in the oral microbiome in the context of industrialization, as the results depend on the oral site under study. Here, we investigated whether microbial communities of dental plaque, the dense biofilm on non-shedding tooth surfaces, are distinctly different across populations with dissimilar subsistence strategies and degree of industrialized market integration. Using a metagenomic approach, we compared the dental plaque microbiomes of Baka foragers and Nzime subsistence agriculturalists in Cameroon (n = 46) with the dental plaque and calculus microbiomes of highly industrialized populations in North America and Europe (n = 38). We found that differences in microbial taxonomic composition between populations were minimal, with high conservation of abundant microbial taxa and no significant differences in microbial diversity related to dietary practices. Instead, we find that the major source of variation in dental plaque microbial species composition is related to tooth location and oxygen availability, which may be influenced by toothbrushing or other dental hygiene measures. Our results support that dental plaque, in contrast to the stool microbiome, maintains an inherent stability against ecological perturbations in the oral environment.}, }
@article {pmid37202726, year = {2023}, author = {Kong, Q and Chen, L and Zeng, X and Lu, F and Huang, Y and Wu, W}, title = {Alterations of the gut microbiome and metabolic profile in CVB3-induced mice acute viral myocarditis.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {139}, pmid = {37202726}, issn = {1471-2180}, abstract = {BACKGROUND: Acute viral myocarditis (AVMC) is an inflammatory disease of the myocardium. Evidence indicates that dysbiosis of gut microbiome and related metabolites intimately associated with cardiovascular diseases through the gut-heart axis.<br><br>METHODS: We built mouse models of AVMC, then applied 16&#xa0;S rDNA gene sequencing and UPLC-MS/MS metabolomics to explore variations of gut microbiome and disturbances of cardiac metabolic profiles.<br><br>RESULTS: Compared with Control group, analysis of gut microbiota showed lower diversity in AVMC, decreased relative abundance of genera mainly belonging to the phyla Bacteroidetes, and increased of phyla Proteobacteria. Metabolomics analysis showed disturbances of cardiac metabolomics, including 62 increased and 84 decreased metabolites, and mainly assigned to lipid, amino acid, carbohydrate and nucleotide metabolism. The steroid hormone biosynthesis, cortisol synthesis and secretion pathway were particularly enriched in AVMC. Among them, such as estrone 3-sulfate, desoxycortone positively correlated with disturbed gut microbiome.<br><br>CONCLUSION: In summary, both the structure of the gut microbiome community and the cardiac metabolome were significantly changed in AVMC. Our findings suggest that gut microbiome may participate in the development of AVMC, the mechanism may be related to its role in dysregulated metabolites such as steroid hormone biosynthesis.}, }
@article {pmid37202560, year = {2023}, author = {Roelands, J and Kuppen, PJK and Ahmed, EI and Mall, R and Masoodi, T and Singh, P and Monaco, G and Raynaud, C and de Miranda, NFCC and Ferraro, L and Carneiro-Lobo, TC and Syed, N and Rawat, A and Awad, A and Decock, J and Mifsud, W and Miller, LD and Sherif, S and Mohamed, MG and Rinchai, D and Van den Eynde, M and Sayaman, RW and Ziv, E and Bertucci, F and Petkar, MA and Lorenz, S and Mathew, LS and Wang, K and Murugesan, S and Chaussabel, D and Vahrmeijer, AL and Wang, E and Ceccarelli, A and Fakhro, KA and Zoppoli, G and Ballestrero, A and Tollenaar, RAEM and Marincola, FM and Galon, J and Khodor, SA and Ceccarelli, M and Hendrickx, W and Bedognetti, D}, title = {An integrated tumor, immune and microbiome atlas of colon cancer.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {37202560}, issn = {1546-170X}, abstract = {The lack of multi-omics cancer datasets with extensive follow-up information hinders the identification of accurate biomarkers of clinical outcome. In this cohort study, we performed comprehensive genomic analyses on fresh-frozen samples from 348 patients affected by primary colon cancer, encompassing RNA, whole-exome, deep T cell receptor and 16S bacterial rRNA gene sequencing on tumor and matched healthy colon tissue, complemented with tumor whole-genome sequencing for further microbiome characterization. A type 1 helper T cell, cytotoxic, gene expression signature, called Immunologic Constant of Rejection, captured the presence of clonally expanded, tumor-enriched T cell clones and outperformed conventional prognostic molecular biomarkers, such as the consensus molecular subtype and the microsatellite instability classifications. Quantification of genetic immunoediting, defined as a lower number of neoantigens than expected, further refined its prognostic value. We identified a microbiome signature, driven by Ruminococcus bromii, associated with a favorable outcome. By combining microbiome signature and Immunologic Constant of Rejection, we developed and validated a composite score (mICRoScore), which identifies a group of patients with excellent survival probability. The publicly available multi-omics dataset provides a resource for better understanding colon cancer biology that could facilitate the discovery of personalized therapeutic approaches.}, }
@article {pmid37202414, year = {2023}, author = {Huggett, MJ and Hobbs, JA and Vitelli, F and Stat, M and Sinclair-Taylor, TH and Bunce, M and DiBattista, JD}, title = {Gut microbial communities of hybridising pygmy angelfishes reflect species boundaries.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {542}, pmid = {37202414}, issn = {2399-3642}, abstract = {Hybridisation and introgression of eukaryotic genomes can generate new species or subsume existing ones, with direct and indirect consequences for biodiversity. An understudied component of these evolutionary forces is their potentially rapid effect on host gut microbiomes, and whether these pliable microcosms may serve as early biological indicators of speciation. We address this hypothesis in a field study of angelfishes (genus Centropyge), which have one of the highest prevalence of hybridisation within coral reef fish. In our study region of the Eastern Indian Ocean, the parent fish species and their hybrids cohabit and display no differences in their diet, behaviour, and reproduction, often interbreeding in mixed harems. Despite this ecological overlap, we show that microbiomes of the parent species are significantly different from each other in form and function based on total community composition, supporting the division of parents into distinct species, despite the confounding effects of introgression acting to homogenize parent species identity at other molecular markers. The microbiome of hybrid individuals, on the other hand, are not significantly different to each of the parents, instead harbouring an intermediate community composition. These findings suggest that shifts in gut microbiomes may be an early indicator of speciation in hybridising species.}, }
@article {pmid37202074, year = {2023}, author = {de Souza Furtado, J and de Almeida Brasiel, PG and Luquetti, SCPD}, title = {Profile of the intestinal microbiota of patients with cystic fibrosis: A systematic review.}, journal = {Clinical nutrition ESPEN}, volume = {55}, number = {}, pages = {400-406}, doi = {10.1016/j.clnesp.2023.04.008}, pmid = {37202074}, issn = {2405-4577}, abstract = {BACKGROUND &amp; AIMS: Cystic fibrosis (CF) is a multisystem disease that can compromise several human body organs. The autosomal recessive genetic disorder is caused by different mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, responsible for chloride ion transport across apical membranes of epithelial cells in tissues and bicarbonate secretion. In this study, we provide a systematic review of the profile of the intestinal microbiota of cystic fibrosis individuals.<br><br>METHODS: The review was conducted according to Preferred Items of Reports for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. PubMed/MEDLINE and Scopus databases were searched for relevant articles until Jully 2022.<br><br>RESULTS: Eighteen studies (1304 participants) met the inclusion criteria. The quality and bias was assessed using the Methodological index for non-randomized studies (MINORS) tool, with the majority of the studies indicating medium to high quality. Results showed significant changes in the composition of the intestinal microbiota of the individuals with CF compared with healthy controls, with increased of Enterococcus, Veillonella, and Streptococcus, and decreased of Bifidobacterium, Roseburia, and Alistipes genus. The intestinal bacterial community of CF patients was marked by a reduction in its richness and diversity.<br><br>CONCLUSION: The systematic review suggests a change in the intestinal microbiota of CF individuals, characterized by a reduction in microbial diversity and abundance of some bacterial markers.}, }
@article {pmid37201857, year = {2023}, author = {Forouzandeh, A and Lassen, SB and Brinck, JE and Zhou, YY and Zhu, J and Solà-Oriol, D and Monteiro, A and Hao, X and Su, JQ and Stein, HH and Pérez, JF and Brandt, KK}, title = {Limited impacts of high doses of dietary copper on the gut bacterial metal resistome explain negligible co-selection of antibiotic resistance.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164183}, doi = {10.1016/j.scitotenv.2023.164183}, pmid = {37201857}, issn = {1879-1026}, abstract = {High dietary intake of Cu has previously been linked to the selection of Cu resistance and co-selection of antibiotic resistance in specific gut bacteria. Based on a novel HT-qPCR metal resistance gene chip as combined with 16S rRNA gene amplicon sequencing and phenotypic resistance typing of Escherichia coli isolates, we here report the impacts of two contrasting Cu-based feed additives on the swine gut bacterial metal resistome and community assembly. DNA was extracted from fecal samples (n = 80) collected at day 26 and 116 of the experiment from 200 pigs allotted to five dietary treatments: negative control (NC) diet with 20 μg CuSO4 g[-1] and four diets added 125 or 250 μg CuSO4 g[-1] feed or 125 or 250 μg Cu2O g[-1] feed to the NC diet. Dietary Cu supplementation reduced the relative abundance of Lactobacillus, but it had negligible impacts on bacterial community composition relative to the gut microbiome maturation effect (time). The relative importance of different bacterial community assembly processes was not markedly affected by the dietary Cu treatments, and differences in swine gut metal resistome composition could be explained primarily by differences in bacterial community composition rather than by dietary Cu treatments. High dietary Cu intake (250 μg Cu g[-1]) selected for phenotypic Cu resistance in E. coli isolates, but surprisingly it did not result in increased prevalence of the Cu resistance genes targeted by the HT-qPCR chip. In conclusion, the lacking impacts of dietary Cu on the gut bacterial metal resistome explain results from a previous study showing that even high therapeutic doses of dietary Cu did not cause co-selection of antibiotic resistance genes and mobile genetic elements known to harbor these genes.}, }
@article {pmid37201821, year = {2023}, author = {Viver, T and Ruiz, A and Bertomeu, E and Martorell-Barceló, M and Urdiain, M and Grau, A and Signaroli, M and Barcelo-Serra, M and Aspillaga, E and Pons, A and Rodgers, C and Gisbert, E and Furones, D and Alós, J and Catalán, IA and Rossello-Mora, R}, title = {Food determines ephemerous and non-stable gut microbiome communities in juvenile wild and farmed Mediterranean fish.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164080}, doi = {10.1016/j.scitotenv.2023.164080}, pmid = {37201821}, issn = {1879-1026}, abstract = {Novel insights were provided by contrasting the composition of wild and farmed fish gut microbiomes because the latter had essentially different environmental conditions from those in the wild. This was reflected in the gut microbiome of the wild Sparus aurata and Xyrichtys novacula studied here, which showed highly diverse microbial community structures, dominated by Proteobacteria, mostly related to an aerobic or microaerophilic metabolism, but with some common shared major species, such as Ralstonia sp. On the other hand, farmed non-fasted S. aurata individuals had a microbial structure that mirrored the microbial composition of their food source, which was most likely anaerobic, since several members of the genus Lactobacillus, probably revived from the feed and enriched in the gut, dominated the communities. The most striking observation was that after a short fasting period (86 h), farmed gilthead seabream almost lost their whole gut microbiome, and the resident community associated with the mucosa had a very much reduced diversity that was highly dominated by a single potentially aerobic species Micrococcus sp., closely related to M. flavus. The results pointed to the fact that, at least for the juvenile S. aurata studied, most of the microbes in the gut were transient and highly dependent on the feed source, and that only after fasting for at least 2 days could the resident microbiome in the intestinal mucosa be determined. Since an important role of this transient microbiome in relation to fish metabolism could not be discarded, the methodological approach needs to be well designed in order not to bias the results. The results have important implications for fish gut studies that could explain the diversity and occasional contradictory results published in relation to the stability of marine fish gut microbiomes, and might provide important information for feed formulation in the aquaculture industry.}, }
@article {pmid37201625, year = {2023}, author = {Chen, G and Wang, Z and Song, W and Liao, Y and Wang, X and Chen, C and Ming, J and Cui, J and Xu, K}, title = {Effects of long-term regular oral aspirin combined with atorvastatin to prevent ischemic stroke on human gut microbiota.}, journal = {European journal of pharmacology}, volume = {}, number = {}, pages = {175800}, doi = {10.1016/j.ejphar.2023.175800}, pmid = {37201625}, issn = {1879-0712}, abstract = {PURPOSE: Every year, there is a large number of people take aspirin and atorvastatin to prevent ischemic stroke, but the effect of these drugs on gut microbiota remains unknown. We aimed to examine the effects of long-term regular oral aspirin with atorvastatin to prevent ischemic stroke on human gut microbiota.<br><br>METHODS: A cross-sectional study of 20 participants with the drugs over one year and the other 20 gender- and age-matching participants without medication were recruited from the Affiliated Hospital of Guizhou Medical University. The medication habits and dietary information were obtained using a questionnaire. Fecal samples collected from all participants were subjected to 16S rRNA sequencing of the microbiome. The datasets were analyzed using bioinformatics approaches.<br><br>RESULTS: The Alpha diversity showed that compared with controls, medication participants had lower ACE and Chao1 index, while no difference in the Shannon index and Simpson index. The Beta diversity analysis revealed significant shifts in the taxonomic compositions of the two groups. Linear discriminant analysis effect size (LEfSe) analysis combined with receiver operating characteristic (ROC) curves revealed the marker bacteria associated with taking medication were g_Parabacteroides&#xff08;AUC&#x202f;=&#x202f;0.855&#xff09;, g_Bifidobacterium&#xff08;AUC&#x202f;=&#x202f;0.815&#xff09;, s_Bifidobacterium_longum_subsp&#xff08;AUC&#x202f;=&#x202f;0.8075&#xff09;, and with no taking medication was g_Prevotella_9&#xff08;AUC&#x202f;=&#x202f;0.76&#xff09;.<br><br>CONCLUSIONS: Our findings indicated that long-term regular oral aspirin and atorvastatin modulate the human gut microbiota. Taking these drugs may affect the preventive effect of ischemic stroke by changing the abundance of specific gut microbiota.}, }
@article {pmid37201335, year = {2023}, author = {Laragione, T and Harris, C and Azizgolshani, N and Beeton, C and Bongers, G and Gulko, PS}, title = {Magnesium increases numbers of Foxp3+ Treg cells and reduces arthritis severity and joint damage in an IL-10-dependent manner mediated by the intestinal microbiome.}, journal = {EBioMedicine}, volume = {92}, number = {}, pages = {104603}, doi = {10.1016/j.ebiom.2023.104603}, pmid = {37201335}, issn = {2352-3964}, abstract = {BACKGROUND: Rheumatoid arthritis (RA) is a common autoimmune disease with emerging environmental and microbiome risk factors. The western diet is typically deficient in magnesium (Mg), and there is some evidence suggesting that Mg may have anti-inflammatory properties. But the actual role of Mg supplementation in arthritis or in T cell subsets has not been explored.<br><br>METHODS: We investigated the role of a high Mg diet in two different mouse models of RA induced with the KRN serum, and collagen-induced arthritis. We also characterized the phenotypes of splenocytes, gene expression, and an extensive intestinal microbiome analyses including fecal material transplantation (FMT).<br><br>FINDINGS: The high Mg diet group was significantly protected with reduced arthritis severity and joint damage, and reduced expression of IL-1&#x3b2;, IL-6, and TNF&#x3b1;. The high Mg group also had increased numbers of Foxp3+ Treg cells and IL-10-producing T cells. The high Mg protective effect disappeared in IL-10 knockout mice. FMT from the high Mg diet mice recreated the phenotypes seen in the diet-treated mice, with reduced arthritis severity, increased Foxp3+ Treg, and increased IL-10-producing T cells. Intestinal microbiome analyses using 16S rDNA sequencing revealed diet-specific changes, including reduced levels of RA-associated Prevotella in the high Mg group, while increasing levels of Bacteroides and other bacteria associated with increased production of short-chain fatty acids. Metagenomic analyses implicated additional pathways including L-tryptophan biosynthesis and arginine deiminase.<br><br>INTERPRETATION: We describe a new role for Mg in suppressing arthritis, in expanding Foxp3+ T reg cells and in the production of IL-10, and show that these effects are mediated by the intestinal microbiome. Our discoveries suggest a novel strategy for modifying the intestinal microbiome to treat RA and other autoimmune and inflammatory diseases.<br><br>FUNDING: None.}, }
@article {pmid37201116, year = {2023}, author = {Dahdouh, E and Cendejas-Bueno, E and Ruiz-Carrascoso, G and Schüffelmann, C and Lázaro-Perona, F and Castro-Martínez, M and Moreno-Ramos, F and Escosa-García, L and Alguacil-Guillén, M and Mingorance, J}, title = {Intestinal loads of extended-spectrum beta-lactamase and Carbapenemase genes in critically ill pediatric patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1180714}, pmid = {37201116}, issn = {2235-2988}, abstract = {INTRODUCTION: Intestinal colonization by Multi-Drug Resistant Organisms (MDROs) can pose a threat on the health of critically ill patients. The extent of colonization by these organisms is related to previous antibiotic treatments and their ability to cause infections among adult patients. The aim of this study is to determine the relationship between the intestinal Relative Loads (RLs) of selected antibiotic resistance genes, antibiotic consumption and extra-intestinal spread among critically ill pediatric patients.<br><br>METHODS: RLs of bla CTX-M-1-Family, bla OXA-1, bla OXA-48 and bla VIM were determined in 382 rectal swabs obtained from 90 pediatric critically ill patients using qPCRs. The RLs were compared to the patients' demographics, antibiotic consumption, and detection of MDROs from extra-intestinal sites. 16SrDNA metagenomic sequencing was performed for 40 samples and clonality analyses were done for representative isolates.<br><br>RESULTS AND DISCUSSION: 76 (74.45%) patients from which 340 (89.01%) rectal swabs were collected had at least one swab that was positive for one of the tested genes. Routine cultures did not identify carbapenemases in 32 (45.1%) and 78 (58.2%) swabs that were positive by PCR for bla OXA-48 and blaVIM, respectively. RLs of above 6.5% were associated with extra-intestinal spread of blaOXA-48-harboring MDROs. Consumption of carbapenems, non-carbapenem &#x3b2;-lactams, and glycopeptides were statistically associated with testing negative for bla CTX-M-1-Family and bla OXA-1 while the consumption of trimethoprim/sulfamethoxazole and aminoglycosides was associated with testing negative for blaOXA-48 (P<0.05). In conclusion, targeted qPCRs can be used to determine the extent of intestinal dominance by antibiotic resistant opportunistic pathogens and their potential to cause extra-intestinal infections among a critically ill pediatric population.}, }
@article {pmid37201112, year = {2023}, author = {Yan, F and Zhang, Q and Shi, K and Zhang, Y and Zhu, B and Bi, Y and Wang, X}, title = {Gut microbiota dysbiosis with hepatitis B virus liver disease and association with immune response.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1152987}, pmid = {37201112}, issn = {2235-2988}, abstract = {BACKGROUND AND AIMS: Given hepatitis B virus (HBV)-related hepatocellular carcinoma (HBV-HCC) exhibits unique gut microbiota characteristics and a significant immunosuppressive tumor microenvironment. Thus, a better understanding of the correlation between gut microbiota and the immunosuppressive response may help predict occurrence and prognosis of HBV-HCC.<br><br>METHODS: Here, in a cohort of ninety adults (healthy control n=30, HBV-cirrhosis n=30, HBV-HCC n=30) with clinical data, fecal 16S rRNA gene sequencing, matched peripheral blood immune response with flow cytometry analysis. Correlation between the gut microbiome of significantly different in HBV-HCC patients and clinical parameters as well as the peripheral immune response was assessed.<br><br>RESULTS: We found that community structures and diversity of the gut microbiota in HBV-CLD patients become more unbalanced. Differential microbiota analysis that p:Acidobacteriota, p:Proteobacteria, p:Campilobacterota, f:Streptococcaceae, g:Klebsiella associated with inflammation were enriched. The beneficial bacteria of f:Clostridia UCG-014, f:Oscillospiraceae, f:_Rikenellaceae, g:_Barnesiella, g:Prevotella, g:Agathobacter were decreased. Functional analysis of gut microbiota revealed that lipopolysaccharide biosynthesis, lipid metabolism, butanoate metabolism were significantly elevated in HBV-CLD patients. Spearman's correlation analysis showed that Muribaculaceae, Akkermaniacaeae, [Eubacterium]_coprostanoligenes_group, RF39, Tannerellaceae have positive correlation with CD3+T, CD4+T and CD8+T cell counts while negatively correlated with liver dysfunction. Furthermore, paired peripheral blood showed a decreased proportion of CD3+T, CD4+T and CD8+T cells, while an increased T (Treg) cells. The immunosuppressive response of programmed cell death 1 (PD-1), cytotoxic T-lymphocyte antigen 4 (CTLA-4), immune receptor tyrosine based inhibitor motor (ITIM) domain (TIGIT), T-cell immune domain, and multiple domain 3 (TIM-3) of CD8+T cells were higher in HBV-HCC patients. They were positively correlated with harmful bacteria, such as Actinobaciota, Myxococota, Streptococcaceae and Eubacterium coprostanoligenes.<br><br>CONCLUSIONS: Our study indicated that gut beneficial bacteria, mainly Firmicutes and Bacteroides appeared dysbiosis in HBV-CLD patients. They have negative regulation of liver dysfunction and T cell immune response. It provides potential avenues for microbiome-based prevention and intervention for anti-tumor immune effects of HBV-CLD.}, }
@article {pmid37200915, year = {2023}, author = {Tang, X and Wang, L and Wang, D and Zhang, Y and Wang, T and Zhu, Z and Weng, Y and Tao, G and Wang, Q and Tang, L and Yan, F and Wang, Y}, title = {Maggot extracts chemo-prevent inflammation and tumorigenesis accompanied by changes in the intestinal microbiome and metabolome in AOM/DSS-induced mice.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1143463}, doi = {10.3389/fmicb.2023.1143463}, pmid = {37200915}, issn = {1664-302X}, abstract = {Inflammatory responses and intestinal microbiome play a crucial role in the progression of colitis-associated carcinoma (CAC). The traditional Chinese medicine maggot has been widely known owing to its clinical application and anti-inflammatory function. In this study, we investigated the preventive effects of maggot extract (ME) by intragastric administration prior to azoxymethane (AOM) and dextran sulfate sodium (DSS)-induced CAC in mice. The results showed that ME had superior advantages in ameliorating disease activity index score and inflammatory phenotype, in comparison with the AOM/DSS group. The number and size of polypoid colonic tumors were decreased after pre-administration of ME. In addition, ME was found to reverse the downregulation of tight junction proteins (zonula occluden-1 and occluding) while suppressing the levels of inflammatory factors (IL-1β and IL-6) in models. Moreover, Toll-like receptor 4 (TLR4) mediated intracellular nuclear factor-κB (NF-κB)-containing signaling cascades, including inducible nitric oxide synthase and cyclooxygenase-2, and exhibited decreasing expression in the mice model after ME pre-administration. 16s rRNA analysis and untargeted-metabolomics profiling of fecal samples inferred that ME revealed ideal prevention of intestinal dysbiosis in CAC mice, accompanied by and correlated with alterations in the composition of metabolites. Overall, ME pre-administration might be a chemo-preventive candidate in the initiation and development of CAC.}, }
@article {pmid37200866, year = {2023}, author = {Tan, X and Wang, Y and Gong, T}, title = {The interplay between oral microbiota, gut microbiota and systematic diseases.}, journal = {Journal of oral microbiology}, volume = {15}, number = {1}, pages = {2213112}, doi = {10.1080/20002297.2023.2213112}, pmid = {37200866}, issn = {2000-2297}, abstract = {Over the past two decades, the importance of microbiota in health and disease has become evident. The human gut microbiota and oral microbiota are the largest and second-largest microbiome in the human body, respectively, and they are physically connected as the oral cavity is the beginning of the digestive system. Emerging and exciting evidence has shown complex and important connections between gut microbiota and oral microbiota. The interplay of the two microbiomes may contribute to the pathological processes of many diseases, including diabetes, rheumatoid arthritis, nonalcoholic fatty liver disease, inflammatory bowel disease, pancreatic cancer, colorectal cancer, and so on. In this review, we discuss possible routes and factors of oral microbiota to affect gut microbiota, and the contribution of this interplay between oral and gut microbiota to systemic diseases. Although most studies are association studies, recently, there have been increasing mechanistic investigations. This review aims to enhance the interest in the connection between oral and gut microbiota, and shows the tangible impact of this connection on human health.}, }
@article {pmid37200786, year = {2023}, author = {Ekadewi, P and Arbianti, R and Gomez, C and Utami, TS}, title = {Biohydrogen Production in Microbial Electrolysis Cell Operating on Designed Consortium of Denitrifying Bacteria.}, journal = {Food technology and biotechnology}, volume = {61}, number = {1}, pages = {4-13}, doi = {10.17113/ftb.61.01.23.7496}, pmid = {37200786}, issn = {1330-9862}, abstract = {RESEARCH BACKGROUND: This study provides insight into the use of a designed microbial community to produce biohydrogen in simple, single-chamber microbial electrolysis cells (MECs). The ability of MECs to stably produce biohydrogen relies heavily on the setup and microorganisms working inside the system. Despite having the most straightforward configuration and effectively avoiding costly membranes, single-chamber MECs are prone to competing metabolic pathways. We present in this study one possible way of avoiding this problem using characteristically defined, designed microbial consortium. Here, we compare the performance of MECs inoculated with a designed consortium to MECs operating with a naturally occurring soil consortium.<br><br>EXPERIMENTAL APPROACH: We adapted a cost-effective and simple single-chamber MEC design. The MEC was gastight, 100 mL in volume, and equipped with continuous monitoring for electrical output using a digital multimeter. Microorganisms were sourced from Indonesian environmental samples, either as denitrifying bacterial isolates grouped as a designed consortium or natural soil microbiome used in its entirety. The designed consortium consisted of five species from the Pseudomonas and Acinetobacter genera. The headspace gas profile was monitored periodically with a gas chromatograph. At the end of the culture, the composition of the natural soil consortium was characterized by next generation sequencing and the growth of the bacteria on the surface of the anodes by field emission scanning electron microscopy.<br><br>RESULTS AND CONCLUSIONS: We found that MEC using a designed consortium presented a better H2 production profile, with the ability of the system to maintain headspace H2 concentration relatively stable for a long time after reaching stationary growth period. In contrast, MECs inoculated with soil microbiome exhibited a strong decline in headspace H2 profile within the same time frame.<br><br>This work utilizes a designed, denitrifying bacterial consortium isolated from Indonesian environmental samples that can survive in a nitrate-rich environment. Here we propose using a designed consortium as a biological approach to avoid methanogenesis in MECs, as a simple and environmentally friendly alternative to current chemical/physical methods. Our findings offer an alternative solution to avoid the problem of H2 loss in single-chamber MECs along with optimizing biohydrogen production through bioelectrochemical routes.}, }
@article {pmid37200323, year = {2023}, author = {Dewayani, A and Afrida Fauzia, K and Alfaray, RI and Waskito, LA and Doohan, D and Rejeki, PS and Alshawsh, MA and Rezkitha, YAA and Yamaoka, Y and Miftahussurur, M}, title = {Gastric microbiome changes in relation with Helicobacter pylori resistance.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0284958}, doi = {10.1371/journal.pone.0284958}, pmid = {37200323}, issn = {1932-6203}, abstract = {INTRODUCTION: Inadequate antimicrobial treatment has led to multidrug-resistant (MDR) bacteria, including Helicobacter pylori (H. pylori), which one of the notable pathogens in the stomach. Antibiotic-induced changes in the microbiota can negatively affect the host. This study aimed to determine the influence of H. pylori resistance on the diversity and abundance of the stomach microbiome.<br><br>METHODS: Bacterial DNA was extracted from biopsy samples of patients presenting dyspepsia symptoms with H. pylori positive from cultures and histology. DNA was amplified from the V3-V4 regions of the 16S rRNA gene. In-vitro E-test was used to detect antibiotic resistance. Microbiome community analysis was conducted through &#x3b1;-diversity, &#x3b2;-diversity, and relative abundance.<br><br>RESULTS: Sixty-nine H. pylori positive samples were eligible after quality filtering. Following resistance status to five antibiotics, samples were classified into 24 sensitive, 24 single resistance, 16 double resistance, 5 triple resistance. Samples were mostly resistant to metronidazole (73.33%; 33/45). Comparation of four groups displayed significantly elevated &#x3b1;-diversity parameters under the multidrug resistance condition (all P <0.05). A notable change was observed in triple-resistant compared to sensitive (P <0.05) and double-resistant (P <0.05) groups. Differences in &#x3b2;-diversity by UniFrac and Jaccard were not significant in terms of the resistance (P = 0.113 and P = 0.275, respectively). In the triple-resistant group, the relative abundance of Helicobacter genera was lower, whereas that of Streptococcus increased. Moreover, the linear discriminant analysis effect size (LEfSe) was associated with the presence of Corynebacterium and Saccharimonadales in the single-resistant group and Pseudomonas and Cloacibacterium in the triple-resistant group.<br><br>CONCLUSION: Our results suggest that the resistant samples showed a higher trend of diversity and evenness than the sensitive samples. The abundance of H. pylori in the triple-resistant samples decreased with increasing cohabitation of pathogenic bacteria, which may support antimicrobial resistance. However, antibiotic susceptibility determined by the E-test may not completely represent the resistance status.}, }
@article {pmid37199986, year = {2023}, author = {Cheng, Z and Shi, J and He, Y and Chen, Y and Wang, Y and Yang, X and Wang, T and Wu, L and Xu, J}, title = {Enhanced soil function and health by soybean root microbial communities during in situ remediation of Cd-contaminated soil with the application of soil amendments.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0104922}, doi = {10.1128/msystems.01049-22}, pmid = {37199986}, issn = {2379-5077}, abstract = {The interactions between soil microbiomes at various trophic levels are essential for restoring soil functions. Legumes are considered as "pioneer crops" in degraded or contaminated soils because they can fix nitrogen through symbiotic relationships with rhizobacteria, which promotes soil fertility. However, little is known about the abilities of legumes to contribute to the health of soil contaminated with Cadmium (Cd). In this research, we applied a soil amendment (commercial Mg-Ca-Si Conditioner, CMC) at two rates (1,500 and 3,000 kg ha[-1]) in a Cd-contaminated soybean field. Bulk and rhizosphere soil samples were collected to assess the amendment-induced effects on four microbial lineages (bacteria, fungi, AMF, and nematodes) and their soil functions including cadmium stabilization, nutrient cycling, and pathogen control. Compared with the control, both CMC application rates increased the pH and reduced labile Cd fraction in the bulk and rhizosphere soils. Although the total Cd concentrations in the soil were similar, the Cd accumulation in the grains was significantly reduced in treatments of soil amendments. It was observed that application of CMC can significantly reduce the AMF diversity, but increase the diversity of other three communities. Moreover, the biodiversity within keystone modules (identified by co-occurrence network analysis) played key roles in driving soil multifunctionality. Specifically, key beneficial groups in module 2 such as Aggregicoccus (Bacteria), Sordariomycetes (Fungi), Glomus (AMF), and Bursaphelenchus (Nematode) were strongly associated with soil multifunctionality. By co-culturing bacterial suspensions with the soybean root rot pathogen Fusarium solani in the in vitro assays, we experimentally validated that application of CMC promoted the suppression of soil bacterial community on pathogens by inhibiting the mycelium growth and spore germination. Also, the bacterial community was more resistant to Cd stress in soils receiving CMC amendment. Our findings provide valuable theoretical references for enhancing soil functions and health via applying a soil amendment (CMC) during Cd-contaminated soil remediation.IMPORTANCERestoration of microbiome-driven soil functions and health is of great importance during Cd-contaminated soil remediation via soil amendment. Soybean and its symbiotic mutualism can provide abundant nitrogen (N) and phosphorus (P) to relieve nutrient deficiency of Cd-contaminated soil. This study provides a novel perspective on the potential role of applying a soil amendment (CMC) in enhancing the functions and health of Cd-contaminated soils. Our results showed the distinct differences in soil microbial community responding to amendment-induced changes in edaphic properties. The biodiversity within keystone modules had major contributions to the maintenance of the soil multifunctionality and health. Additionally, higher CMC application rate showed more beneficial effects. Collectively, our results enhance our understanding about the effects of applying CMC, together with soybean rotation, to enhance and maintain soil functions and health during the field Cd stabilization process.}, }
@article {pmid37199751, year = {2023}, author = {Dixit, S and Varshney, S and Gupta, D and Sharma, S}, title = {Textiles as fomites in the healthcare system.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {37199751}, issn = {1432-0614}, abstract = {Nosocomial infections or healthcare-associated infections (HAIs) are acquired under medical care in healthcare facilities. In hospital environments, the transmission of infectious diseases through textiles such as white coats, bed linen, curtains, and towels are well documented. Textile hygiene and infection control measures have become more important in recent years due to the growing concerns about textiles as fomites in healthcare settings. However, systematic research in this area is lacking; the factors contributing to the transmission of infections through textiles needs to be better understood. The review aims to critically explore textiles as contaminants in healthcare systems, and to identify potential risks they may pose to patients and healthcare workers. It delineates different factors affecting bacterial adherence on fabrics, such as surface properties of bacteria and fabrics, and environmental factors. It also identifies areas that require further research to reduce the risk of HAIs and improve textile hygiene practices. Finally, the review elaborates on the strategies currently employed, and those that can be employed to limit the spread of nosocomial infections through fabrics. Implementing textile hygiene practices effectively in healthcare facilities requires a thorough analysis of factors affecting fabric-microbiome interactions, followed by designing newer fabrics that discourage pathogen load. KEY POINTS: • Healthcare textiles act as a potential reservoir of nosocomial pathogens • Survival of pathogens is affected by surface properties of fabric and bacteria • Guidelines required for fabrics that discourage microbial load, for hospital use.}, }
@article {pmid37199657, year = {2023}, author = {Sylvain, F&#xc9; and Bouslama, S and Holland, A and Leroux, N and Mercier, PL and Val, AL and Derome, N}, title = {Bacterioplankton Communities in Dissolved Organic Carbon-Rich Amazonian Black Water.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0479322}, doi = {10.1128/spectrum.04793-22}, pmid = {37199657}, issn = {2165-0497}, abstract = {The Amazon River basin sustains dramatic hydrochemical gradients defined by three water types: white, clear, and black waters. In black water, important loads of allochthonous humic dissolved organic matter (DOM) result from the bacterioplankton degradation of plant lignin. However, the bacterial taxa involved in this process remain unknown, since Amazonian bacterioplankton has been poorly studied. Its characterization could lead to a better understanding of the carbon cycle in one of the Earth's most productive hydrological systems. Our study characterized the taxonomic structure and functions of Amazonian bacterioplankton to better understand the interplay between this community and humic DOM. We conducted a field sampling campaign comprising 15 sites distributed across the three main Amazonian water types (representing a gradient of humic DOM), and a 16S rRNA metabarcoding analysis based on bacterioplankton DNA and RNA extracts. Bacterioplankton functions were inferred using 16S rRNA data in combination with a tailored functional database from 90 Amazonian basin shotgun metagenomes from the literature. We discovered that the relative abundances of fluorescent DOM fractions (humic-, fulvic-, and protein-like) were major drivers of bacterioplankton structure. We identified 36 genera for which the relative abundance was significantly correlated with humic DOM. The strongest correlations were found in the Polynucleobacter, Methylobacterium, and Acinetobacter genera, three low abundant but omnipresent taxa that possessed several genes involved in the main steps of the β-aryl ether enzymatic degradation pathway of diaryl humic DOM residues. Overall, this study identified key taxa with DOM degradation genomic potential, the involvement of which in allochthonous Amazonian carbon transformation and sequestration merits further investigation. IMPORTANCE The Amazon basin discharge carries an important load of terrestrially derived dissolved organic matter (DOM) to the ocean. The bacterioplankton from this basin potentially plays important roles in transforming this allochthonous carbon, which has consequences on marine primary productivity and global carbon sequestration. However, the structure and function of Amazonian bacterioplanktonic communities remain poorly studied, and their interactions with DOM are unresolved. In this study, we (i) sampled bacterioplankton in all the main Amazon tributaries, (ii) combined information from the taxonomic structure and functional repertory of Amazonian bacterioplankton communities to understand their dynamics, (iii) identified the main physicochemical parameters shaping bacterioplanktonic communities among a set of >30 measured environmental parameters, and (iv) characterized how bacterioplankton structure varies according to the relative abundance of humic compounds, a by-product from the bacterial degradation process of allochthonous DOM.}, }
@article {pmid37199656, year = {2023}, author = {Raj, Y and Kumar, A and Kumari, S and Kumar, R and Kumar, R}, title = {Comparative Genomics and Physiological Investigations Supported Multifaceted Plant Growth-Promoting Activities in Two Hypericum perforatum L.-Associated Plant Growth-Promoting Rhizobacteria for Microbe-Assisted Cultivation.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0060723}, doi = {10.1128/spectrum.00607-23}, pmid = {37199656}, issn = {2165-0497}, abstract = {Plants are no longer considered standalone entities; instead, they harbor a diverse community of plant growth-promoting rhizobacteria (PGPR) that aid them in nutrient acquisition and can also deliver resilience. Host plants recognize PGPR in a strain-specific manner; therefore, introducing untargeted PGPR might produce unsatisfactory crop yields. Consequently, to develop a microbe-assisted Hypericum perforatum L. cultivation technique, 31 rhizobacteria were isolated from the plant's high-altitude Indian western Himalayan natural habitat and in vitro characterized for multiple plant growth-promoting attributes. Among 31 rhizobacterial isolates, 26 produced 0.59 to 85.29 μg mL[-1] indole-3-acetic acid and solubilized 15.77 to 71.43 μg mL[-1] inorganic phosphate; 21 produced 63.12 to 99.92% siderophore units, and 15 exhibited 103.60 to 1,296.42 nmol α-ketobutyrate mg[-1] protein h[-1] 1-aminocyclopropane-1-carboxylate deaminase (ACCD) activity. Based on superior plant growth-promoting attributes, eight statistically significant multifarious PGPR were further evaluated for an in planta plant growth-promotion assay under poly greenhouse conditions. Plants treated with Kosakonia cowanii HypNH10 and Rahnella variigena HypNH18 showed, by significant amounts, the highest photosynthetic pigments and performance, eventually leading to the highest biomass accumulation. Comparative genome analysis and comprehensive genome mining unraveled their unique genetic features, such as adaptation to the host plant's immune system and specialized metabolites. Moreover, the strains harbor several functional genes regulating direct and indirect plant growth-promotion mechanisms through nutrient acquisition, phytohormone production, and stress alleviation. In essence, the current study endorsed strains HypNH10 and HypNH18 as cogent candidates for microbe-assisted H. perforatum cultivation by highlighting their exclusive genomic signatures, which suggest their unison, compatibility, and multifaceted beneficial interactions with their host and support the excellent plant growth-promotion performance observed in the greenhouse trial. IMPORTANCE Hypericum perforatum L. (St. John's wort) herbal preparations are among the top-selling products to treat depression worldwide. A significant portion of the overall Hypericum supply is sourced through wild collection, prompting a rapid decline in their natural stands. Crop cultivation seems lucrative, although cultivable land and its existing rhizomicrobiome are well suited for traditional crops, and its sudden introduction can create soil microbiome dysbiosis. Also, the conventional plant domestication procedures with increased reliance on agrochemicals can reduce the diversity of the associated rhizomicrobiome and plants' ability to interact with plant growth-promoting microorganisms, leading to unsatisfactory crop production alongside harmful environmental effects. Cultivating H. perforatum with crop-associated beneficial rhizobacteria can reconcile such concerns. Based on a combinatorial in vitro, in vivo plant growth-promotion assay and in silico prediction of plant growth-promoting traits, here we recommend two H. perforatum-associated PGPR, Kosakonia cowanii HypNH10 and Rahnella variigena HypNH18, to extrapolate as functional bioinoculants for H. perforatum sustainable cultivation.}, }
@article {pmid37199635, year = {2023}, author = {Tao, Z and Chen, Y and He, F and Tang, J and Zhan, L and Hu, H and Ding, Z and Ruan, S and Chen, Y and Chen, B and Wang, Y and Guo, X and Xie, L and Zhong, M and Huang, Q}, title = {Alterations in the Gut Microbiome and Metabolisms in Pregnancies with Fetal Growth Restriction.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0007623}, doi = {10.1128/spectrum.00076-23}, pmid = {37199635}, issn = {2165-0497}, abstract = {Fetuses diagnosed with fetal growth restriction (FGR) are at an elevated risk of stillbirth and adulthood morbidity. Gut dysbiosis has emerged as one of the impacts of placental insufficiency, which is the main cause of FGR. This study aimed to characterize the relationships among the intestinal microbiome, metabolites, and FGR. Characterization was conducted on the gut microbiome, fecal metabolome, and human phenotypes in a cohort of 35 patients with FGR and 35 normal pregnancies (NP). The serum metabolome was analyzed in 19 patients with FGR and 31 normal pregnant women. Multidimensional data was integrated to reveal the links between data sets. A fecal microbiota transplantation mouse model was used to determine the effects of the intestinal microbiome on fetal growth and placental phenotypes. The diversity and composition of the gut microbiota were altered in patients with FGR. A group of microbial species altered in FGR closely correlated with fetal measurements and maternal clinical variables. Fecal and serum metabolism profiles were distinct in FGR patients compared to those in the NP group. Altered metabolites were identified and associated with clinical phenotypes. Integrated multi-omics analysis revealed the interactions among gut microbiota, metabolites, and clinical measurements. Microbiota from FGR gravida transplanted to mice progestationally induced FGR and placental dysfunction, including impaired spiral artery remodeling and insufficient trophoblast cell invasion. Taken together, the integration of microbiome and metabolite profiles from the human cohort indicates that patients with FGR endure gut dysbiosis and metabolic disorders, which contribute to disease pathogenesis. IMPORTANCE Downstream of the primary cause of fetal growth restriction are placental insufficiency and fetal malnutrition. Gut microbiota and metabolites appear to play an important role in the progression of gestation, while dysbiosis induces maternal and fetal complications. Our study elaborates the significant differences in microbiota profiles and metabolome characteristics between women with FGR and normal pregnancies. This is the first attempt so far that reveals the mechanistic links in multi-omics in FGR, providing a novel insight into host-microbe interaction in placenta-derived diseases.}, }
@article {pmid37199629, year = {2023}, author = {Leão, I and Khalifa, L and Gallois, N and Vaz-Moreira, I and Klümper, U and Youdkes, D and Palmony, S and Dagai, L and Berendonk, TU and Merlin, C and Manaia, CM and Cytryn, E}, title = {Microbiome and Resistome Profiles along a Sewage-Effluent-Reservoir Trajectory Underline the Role of Natural Attenuation in Wastewater Stabilization Reservoirs.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0017023}, doi = {10.1128/aem.00170-23}, pmid = {37199629}, issn = {1098-5336}, abstract = {Antibiotic-resistant bacteria and antibiotic resistance gene (ARGs) loads dissipate through sewage treatment plants to receiving aquatic environments, but the mechanisms that mitigate the spread of these ARGs are not well understood due to the complexity of full-scale systems and the difficulty of source tracking in downstream environments. To overcome this problem, we targeted a controlled experimental system comprising a semicommercial membrane-aerated bioreactor (MABR), whose effluents fed a 4,500-L polypropylene basin that mimicked effluent stabilization reservoirs and receiving aquatic ecosystems. We analyzed a large set of physicochemical measurements, concomitant with the cultivation of total and cefotaxime-resistant Escherichia coli, microbial community analyses, and quantitative PCR (qPCR)/digital droplet PCR (ddPCR) quantification of selected ARGs and mobile genetic elements (MGEs). The MABR removed most of the sewage-derived organic carbon and nitrogen, and simultaneously, E. coli, ARG, and MGE levels dropped by approximately 1.5- and 1.0-log unit mL[-1], respectively. Similar levels of E. coli, ARGs, and MGEs were removed in the reservoir, but interestingly, unlike in the MABR, the relative abundance (normalized to 16S rRNA gene-inferred total bacterial abundance) of these genes also decreased. Microbial community analyses revealed the substantial shifts in bacterial and eukaryotic community composition in the reservoir relative to the MABR. Collectively, our observations lead us to conclude that the removal of ARGs in the MABR is mainly a consequence of treatment-facilitated biomass removal, whereas in the stabilization reservoir, mitigation is linked to natural attenuation associated with ecosystem functioning, which includes abiotic parameters, and the development of native microbiomes that prevent the establishment of wastewater-derived bacteria and associated ARGs. IMPORTANCE Wastewater treatment plants are sources of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs), which can contaminate receiving aquatic environments and contribute to antibiotic resistance. We focused on a controlled experimental system comprising a semicommercial membrane-aerated bioreactor (MABR) that treated raw sewage, whose effluents fed a 4,500-L polypropylene basin that mimicked effluent stabilization reservoirs. We evaluated ARB and ARG dynamics across the raw-sewage-MABR-effluent trajectory, concomitant with evaluation of microbial community composition and physicochemical parameters, in an attempt to identify mechanisms associated with ARB and ARG dissipation. We found that removal of ARB and ARGs in the MABR was primarily associated with bacterial death or sludge removal, whereas in the reservoir it was attributed to the inability of ARBs and associated ARGs to colonize the reservoir due to a dynamic and persistent microbial community. The study demonstrates the importance of ecosystem functioning in removing microbial contaminants from wastewater.}, }
@article {pmid37199622, year = {2023}, author = {Kristensen, M and de Koff, EM and Chu, ML and Groendijk, S and Tramper-Stranders, GA and de Winter-de Groot, KM and Janssens, HM and Tiddens, HA and van Westreenen, M and Sanders, EAM and Arets, BHGM and van der Ent, CK and Prevaes, SMPJ and Bogaert, D}, title = {16S rRNA-Based Microbiota Profiling Assists Conventional Culture Analysis of Airway Samples from Pediatric Cystic Fibrosis Patients.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0405722}, doi = {10.1128/spectrum.04057-22}, pmid = {37199622}, issn = {2165-0497}, abstract = {16S-based sequencing provides broader information on the respiratory microbial community than conventional culturing. However, it (often) lacks species- and strain-level information. To overcome this issue, we used 16S rRNA-based sequencing results from 246 nasopharyngeal samples obtained from 20 infants with cystic fibrosis (CF) and 43 healthy infants, which were all 0 to 6 months old, and compared them to both standard (blind) diagnostic culturing and a 16S-sequencing-informed "targeted" reculturing approach. Using routine culturing, we almost uniquely detected Moraxella catarrhalis, Staphylococcus aureus, and Haemophilus influenzae (42%, 38%, and 33% of samples, respectively). Using the targeted reculturing approach, we were able to reculture 47% of the top-5 operational taxonomical units (OTUs) in the sequencing profiles. In total, we identified 60 species from 30 genera with a median of 3 species per sample (range, 1 to 8). We also identified up to 10 species per identified genus. The success of reculturing the top-5 genera present from the sequencing profile depended on the genus. In the case of Corynebacterium being in the top 5, we recultured them in 79% of samples, whereas for Staphylococcus, this value was only 25%. The success of reculturing was also correlated with the relative abundance of those genera in the corresponding sequencing profile. In conclusion, revisiting samples using 16S-based sequencing profiles to guide a targeted culturing approach led to the detection of more potential pathogens per sample than conventional culturing and may therefore be useful in the identification and, consequently, treatment of bacteria considered relevant for the deterioration or exacerbation of disease in patients like those with CF. IMPORTANCE Early and effective treatment of pulmonary infections in cystic fibrosis is vital to prevent chronic lung damage. Although microbial diagnostics and treatment decisions are still based on conventional culture methods, research is gradually focusing more on microbiome and metagenomic-based approaches. This study compared the results of both methods and proposed a way to combine the best of both worlds. Many species can relatively easily be recultured based on the 16S-based sequencing profile, and it provides more in-depth information about the microbial composition of a sample than that obtained through routine (blind) diagnostic culturing. Still, well-known pathogens can be missed by both routine diagnostic culture methods as well as by targeted reculture methods, sometimes even when they are highly abundant, which may be a consequence of either sample storage conditions or antibiotic treatment at the time of sampling.}, }
@article {pmid37199621, year = {2023}, author = {Qin, H and Jiao, J and A, D and Hua, M and Han, K and Du, H and Wang, Z and Li, J and Zhang, D and Xiao, B and Chen, C}, title = {Single-Molecule Approach to 16S rRNA for Vaginal Microbiome Signatures in Response to Metronidazole Treatment.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0170622}, doi = {10.1128/spectrum.01706-22}, pmid = {37199621}, issn = {2165-0497}, abstract = {Bacterial vaginosis (BV) is the most common infection of the lower reproductive tract among women of reproductive age, characterized by a depletion of health-associated Lactobacillus and an overgrowth of anaerobes. Metronidazole has been recommended as a first-line therapy for treating BV for decades. Although most cases are cured by the treatment, recurrent infections of BV seriously affect women's reproductive health. Until now, limited information on the vaginal microbiota has been explored at the species level. Here, we adopted a single molecular sequencing approach for the 16S rRNA gene, named FLAST (full-length assembly sequencing technology), to analyze the human vaginal microbiota that improved species-level resolution for taxonomy and identified microbiota alterations in the vaginal tract in response to treatment with metronidazole. Appling high-throughput sequencing, we identified 96 and 189 novel full-length 16S rRNA gene sequences in Lactobacillus and Prevotella, respectively, which had not previously been reported in vaginal samples. Moreover, we found that Lactobacillus iners was significantly enriched in the cured group before metronidazole treatment, and that was maintained in a high frequency after the treatment, suggesting an important role for this species in response to metronidazole treatment. Our research also highlights the importance of the single-molecule paradigm for progressing the field of microbiology and applying these insights to better understand the dynamic microbiota during BV treatment. Subsequent novel treatment approaches should be proposed to improve BV treatment outcomes, optimize the vaginal microbiome, and reduce gynecological and obstetric sequelae. IMPORTANCE Bacterial vaginosis (BV) is a common infectious disease of the reproductive tract. Metronidazole treatment, as the first line of treatment, frequently fails at recovery of the microbiome. However, the precise types of Lactobacillus and other bacteria involved in BV remain unclear, and this has resulted in a failure to identify potential markers to predict clinic outcomes. In this study, we adopted a 16S rRNA gene full-length assembly sequencing technology for the taxonomy analysis and evaluation of vaginal microbiota before and after treatment with metronidazole. We additionally identified 96 and 189 novel 16S rRNA gene sequences in Lactobacillus and Prevotella species, respectively, in vaginal samples, which improves our understanding of the vaginal microbiota. Moreover, we found that the abundance of Lactobacillus iners and Prevotella bivia before treatment was associated with a lack of cure. These potential biomarkers will help to facilitate future studies aimed at improving BV treatment outcomes, optimize the vaginal microbiome, and reduce adverse sexual and reproductive outcomes.}, }
@article {pmid37199618, year = {2023}, author = {Liu, J and Fang, H and Hong, N and Lv, C and Zhu, Q and Feng, Y and Wang, B and Tian, J and Yu, Y}, title = {Gut Microbiome and Metabonomic Profile Predict Early Remission to Anti-Integrin Therapy in Patients with Moderate to Severe Ulcerative Colitis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0145723}, doi = {10.1128/spectrum.01457-23}, pmid = {37199618}, issn = {2165-0497}, abstract = {Patients with ulcerative colitis (UC) have low response rates to anti-integrin medications, necessitating the identification of noninvasive biomarkers for predicting remission to anti-integrin therapy. In this study, patients with moderate to severe UC commencing anti-integrin therapy (n = 29), inactive to mild UC patients (n = 13), and healthy controls (n = 11) were selected. Besides clinical evaluation, fecal samples were collected at baseline and week 14 from moderate to severe UC patients. The clinical remission was defined based on the Mayo score. Fecal samples were assessed with 16S rRNA gene sequencing, liquid chromatography-tandem mass spectrometry, and gas chromatography-mass spectrometry (GC-MS). We identified that Verrucomicrobiota was significantly more abundant in the remission group (P < 0.001) than that of nonremission group at phylum level for patients commencing vedolizumab. GC-MS analysis revealed that the concentrations of butyric acid (P = 0.024) and isobutyric acid (P = 0.042) were significantly higher in the remission group compared to the nonremission group at baseline. Finally, the combination of Verrucomicrobiota, butyric acid, and isobutyric acid improved the diagnosis of early remission to anti-integrin therapy (area under the concentration-time curve = 0.961). We identified significantly higher phylum level diversity of Verrucomicrobiota in remission than the nonremission groups at baseline. Notably, the combination of gut microbiome and metabonomic profiles improved the diagnosis of early remission to anti-integrin therapy. IMPORTANCE It is reported that patients with ulcerative colitis (UC) have low response rates to anti-integrin medications in the latest VARSITY study. Therefore, our primary goals were to discover differences in the gut microbiome and metabonomics patterns between early remission and nonremission patients and to explore the diagnostic value in predicting clinical remission to anti-integrin therapy accurately. In this study, we found that Verrucomicrobiota was significantly more abundant in the remission group (P < 0.001) than that of nonremission group at phylum level for patients commencing vedolizumab. Gas chromatography-mass spectrometry analysis revealed that the concentrations of butyric acid (P = 0.024) and isobutyric acid (P = 0.042) were significantly higher in the remission group compared with the nonremission group at baseline. Notably, the combination of Verrucomicrobiota, butyric acid, and isobutyric acid improved the diagnosis of early remission to anti-integrin therapy (area under the concentration-time curve = 0.961).}, }
@article {pmid37199608, year = {2023}, author = {Finlayson-Trick, E and Nearing, J and Fischer, JA and Ma, Y and Wang, S and Krouen, H and Goldfarb, DM and Karakochuk, CD}, title = {The Effect of Oral Iron Supplementation on Gut Microbial Composition: a Secondary Analysis of a Double-Blind, Randomized Controlled Trial among Cambodian Women of Reproductive Age.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0527322}, doi = {10.1128/spectrum.05273-22}, pmid = {37199608}, issn = {2165-0497}, abstract = {The World Health Organization recommends untargeted iron supplementation for women of reproductive age (WRA) in countries where anemia prevalence is greater than 40%, such as Cambodia. Iron supplements, however, often have poor bioavailability, so the majority remains unabsorbed in the colon. The gut houses many iron-dependent bacterial enteropathogens; thus, providing iron to individuals may be more harmful than helpful. We examined the effects of two oral iron supplements with differing bioavailability on the gut microbiomes in Cambodian WRA. This study is a secondary analysis of a double-blind, randomized controlled trial of oral iron supplementation in Cambodian WRA. For 12 weeks, participants received ferrous sulfate, ferrous bisglycinate, or placebo. Participants provided stool samples at baseline and 12 weeks. A subset of stool samples (n = 172), representing the three groups, were randomly selected for gut microbial analysis by 16S rRNA gene sequencing and targeted real-time PCR (qPCR). At baseline, 1% of women had iron-deficiency anemia. The most abundant gut phyla were Bacteroidota (45.7%) and Firmicutes (42.1%). Iron supplementation did not alter gut microbial diversity. Ferrous bisglycinate increased the relative abundance of Enterobacteriaceae, and there was a trend towards an increase in the relative abundance of Escherichia-Shigella. qPCR detected an increase in the enteropathogenic Escherichia coli (EPEC) virulence gene, bfpA, in the group that received ferrous sulfate. Thus, iron supplementation did not affect overall gut bacterial diversity in predominantly iron-replete Cambodian WRA, however, evidence does suggest an increase in relative abundance within the broad family Enterobacteriaceae associated with ferrous bisglycinate use. IMPORTANCE To the best of our knowledge, this is the first published study to characterize the effects of oral iron supplementation on the gut microbiomes of Cambodian WRA. Our study found that iron supplementation with ferrous bisglycinate increases the relative abundance of Enterobacteriaceae, which is a family of bacteria that includes many Gram-negative enteric pathogens like Salmonella, Shigella, and Escherichia coli. Using qPCR for additional analysis, we were able to detect genes associated with enteropathogenic E. coli, a type of diarrheagenic E. coli known to be present around the world, including water systems in Cambodia. The current WHO guidelines recommend blanket (untargeted) iron supplementation for Cambodian WRA despite a lack of studies in this population examining iron's effect on the gut microbiome. This study can facilitate future research that may inform evidence-based global practice and policy.}, }
@article {pmid37199579, year = {2023}, author = {Waldbaum, JDH and Xhumari, J and Akinsuyi, OS and Arjmandi, B and Anton, S and Roesch, LFW}, title = {Association between Dysbiosis in the Gut Microbiota of Primary Osteoporosis Patients and Bone Loss.}, journal = {Aging and disease}, volume = {}, number = {}, pages = {}, doi = {10.14336/AD.2023.0425}, pmid = {37199579}, issn = {2152-5250}, abstract = {In recent decades, gut microbiome research has experienced significant growth, driven by technological advances that enable quantifying bacterial taxa with greater precision. Age, diet, and living environment have emerged as three key factors influencing gut microbes. Dysbiosis, resulting from alterations in these factors, may lead to changes in bacterial metabolites that regulate pro- and anti-inflammatory processes and consequently impact bone health. Restoration of a healthy microbiome signature could mitigate inflammation and potentially reduce bone loss associated with osteoporosis or experienced by astronauts during spaceflight. However, current research is hindered by contradictory findings, insufficient sample sizes, and inconsistency in experimental conditions and controls. Despite progress in sequencing technology, defining a healthy gut microbiome across global populations remains elusive. Challenges persist in identifying accurate gut bacterial metabolics, specific taxa, and their effects on host physiology. We suggest greater attention be directed towards this issue in Western countries as the cost of treating osteoporosis in the United States reaches billions of dollars annually, with expenses projected to continue rising.}, }
@article {pmid37199568, year = {2023}, author = {Kuhn, L and Wang, T and Li, F and Strehlau, R and Tobin, NH and Violari, A and Brooker, S and Patel, F and Liberty, A and Shiau, S and Arpadi, SM and Wadhwa, S and Yin, MT and Wang, S and Tiemessen, CT and Aldrovandi, GM}, title = {Microbiota in the oral cavity of school-age children living with HIV who started antiretroviral therapy at young ages in South Africa.}, journal = {AIDS (London, England)}, volume = {}, number = {}, pages = {}, doi = {10.1097/QAD.0000000000003599}, pmid = {37199568}, issn = {1473-5571}, abstract = {BACKGROUND: Infancy is an important developmental period when the microbiome is shaped. We hypothesized that earlier antiretroviral therapy (ART) initiation would attenuate HIV effects on microbiota in the mouth.<br><br>METHODS: Oral swabs were collected from 477 children living with HIV (CLWH) and 123 children without (controls) at two sites in Johannesburg, South Africa. CLWH had started ART <3&#x200a;years of age; 63% <6&#x200a;months of age. Most were well-controlled on ART at median age 11&#x200a;years when the swab was collected. Controls were age-matched and recruited from the same communities. Sequencing of V4 amplicon of 16S rRNA was done. Differences in microbial diversity and relative abundances of taxa were compared between groups.<br><br>RESULTS: CLWH had lower alpha diversity than controls. Genus-level abundances of Granulicatella, Streptococcus and Gemella were greater and Neisseria and Haemophilus less abundant among CLWH than controls. Associations were stronger among boys. Associations were not attenuated with earlier ART initiation. Shifts in genus-level taxa abundances in CLWH relative to controls were most marked in children on lopinavir/ritonavir regimens; with fewer shifts seen if on efavirenz ART regimens.<br><br>CONCLUSIONS: A distinct profile of less diverse oral bacterial taxa was observed in school-aged CLWH on ART compared to uninfected controls suggesting modulation of microbiota in the mouth by HIV and/or its treatments. Earlier ART initiation was not associated with microbiota profile. Proximal factors, including current ART regimen, were associated with contemporaneous profile of oral microbiota and may have masked associations with distal factors like age at ART initiation.}, }
@article {pmid37199567, year = {2023}, author = {Luo, K and Wang, Z and Peters, BA and Hanna, DB and Wang, T and Sollecito, CC and Grassi, E and Wiek, F and Peter, LS and Usyk, M and Post, WS and Landay, AL and Hodis, HN and Weber, KM and French, A and Golub, ET and Lazar, J and Gustafson, D and Sharma, A and Anastos, K and Clish, CB and Knight, R and Kaplan, RC and Burk, RD and Qi, Q}, title = {Tryptophan metabolism, gut microbiota, and carotid artery plaque in women with and without HIV infection.}, journal = {AIDS (London, England)}, volume = {}, number = {}, pages = {}, doi = {10.1097/QAD.0000000000003596}, pmid = {37199567}, issn = {1473-5571}, abstract = {OBJECTIVE: The perturbation of tryptophan (TRP) metabolism has been linked with HIV infection and cardiovascular disease (CVD), but the interrelationship among TRP metabolites, gut microbiota, and atherosclerosis remain unclear in the context of HIV infection.<br><br>METHODS: We included 361 women (241 HIV+, 120 HIV-) with carotid artery plaque assessments from the Women's Interagency HIV Study, measured ten plasma TRP metabolites and profiled fecal gut microbiome. TRP metabolites-related gut bacteria were selected through the Analysis of Compositions of Microbiomes with Bias Correction method. Associations of TRP metabolites and related microbial features with plaque were examined using multivariable logistic regression.<br><br>RESULTS: While plasma kynurenic acid (KYNA) (odds ratio [OR]&#x200a;=&#x200a;1.93, 95% confidence interval [CI]:1.12, 3.32 per one SD increase; P&#x200a;=&#x200a;0.02) and KYNA/TRP (OR&#x200a;=&#x200a;1.83 [95%CI:1.08, 3.09], P&#x200a;=&#x200a;0.02) were positively associated with plaque, indole-3-propionate (IPA) (OR&#x200a;=&#x200a;0.62 [95%CI:0.40, 0.98], P&#x200a;=&#x200a;0.03) and IPA/KYNA (OR&#x200a;=&#x200a;0.51[95%CI:0.33, 0.80], P&#x200a;<&#x200a;0.01) were inversely associated with plaque. Five gut bacterial genera and many affiliated species were positively associated with IPA (FDR-q&#x200a;<&#x200a;0.25), including Roseburia sp., Eubacterium sp., Lachnospira sp., and Coprobacter sp.; but no bacterial genera were found to be associated with KYNA. Furthermore, an IPA-associated-bacteria score was inversely associated with plaque (OR&#x200a;=&#x200a;0.47[95%CI:0.28, 0.79], P&#x200a;<&#x200a;0.01). But no significant effect modification by HIV serostatus was observed in these associations.<br><br>CONCLUSIONS: In a cohort of women living with and without HIV infection, plasma IPA levels and related gut bacteria were inversely associated with carotid artery plaque, suggesting a potential beneficial role of IPA and its gut bacterial producers in atherosclerosis and CVD.}, }
@article {pmid37199526, year = {2023}, author = {Bundgaard-Nielsen, C and Lauritsen, MB and Knudsen, JK and Rold, LS and Larsen, MH and Hindersson, P and Villadsen, AB and Leutscher, PDC and Hagstrøm, S and Nyegaard, M and Sørensen, S}, title = {Children and adolescents with attention deficit hyperactivity disorder and autism spectrum disorder share distinct microbiota compositions.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2211923}, doi = {10.1080/19490976.2023.2211923}, pmid = {37199526}, issn = {1949-0984}, abstract = {An association has been suggested between altered gut microbiota, and attention deficit hyperactivity disorder (ADHD), and autism spectrum disorder (ASD), respectively. Thus, we analyzed the gut microbiota composition in children and adolescents with or without these disorders and evaluated the systemic effects of these bacteria. We recruited study participants diagnosed with ADHD, ASD, and comorbid ADHD/ASD, while the control groups consisted both of siblings and non-related children. The gut microbiota was analyzed by 16S rRNA gene sequencing of the V4 region, while the concentration of lipopolysaccharide-binding protein (LBP), cytokines, and other signaling molecules were measured in plasma. Importantly the gut microbiota compositions of cases with ADHD and ASD were highly similar for both alpha- and beta-diversity while differing from that of non-related controls. Furthermore, a subset of ADHD and ASD cases had an increased LBP concentration compared to non-affected children, which was positively correlated with interleukin (IL)-8, 12, and 13. These observations indicate disruption of the intestinal barrier and immune dysregulation among the subset of children with ADHD or ASD.}, }
@article {pmid37199247, year = {2023}, author = {Sohn, KH and Choi, S and Jung, JW and Choi, JH and Cho, SH and Yi, H and Kang, HR}, title = {Different inflammatory features of asthma according to gut microbiome enterotype.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.15768}, pmid = {37199247}, issn = {1398-9995}, }
@article {pmid37198716, year = {2023}, author = {Ding, EM and Wang, JN and Deng, FC and Sun, PJ and Li, CF and Li, CL and Wang, Y and Fang, JL and Tang, S and Shi, XM}, title = {[A panel study on the effect of atmospheric PM2.5 exposure on the gut microbiome in healthy elderly people aged 60-69 years old].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {57}, number = {}, pages = {1-8}, doi = {10.3760/cma.j.cn112150-20230220-00133}, pmid = {37198716}, issn = {0253-9624}, abstract = {Objective: To analyze the short-term effect of individual atmospheric PM2.5 exposure on the diversity, enterotype, and community structure of gut microbiome in healthy elderly people in Jinan, Shandong province. Methods: The present panel study recruited 76 healthy elderly people aged 60-69 years old in Dianliu Street, Lixia District, Jinan, Shandong Province, and followed them up five times from September 2018 to January 2019. The relevant information was collected by questionnaire, physical examination, precise monitoring of individual PM2.5 exposure, fecal sample collection and gut microbiome 16S rDNA sequencing. The Dirichlet multinomial mixtures (DMM) model was used to analyze the enterotype. Linear mixed effect model and generalized linear mixed effect model were used to analyze the effect of PM2.5 exposure on gut microbiome α diversity indices (Shannon, Simpson, Chao1, and ACE indices), enterotype and abundance of core species. Results: Each of the 76 subjects participated in at least two follow-up visits, resulting in a total of 352 person-visits. The age of 76 subjects was (65.0±2.8) years old with BMI (25.0±2.4) kg/m[2]. There were 38 males accounting for 50% of the subjects. People with an educational level of primary school or below accounted for 10.5% of the 76 subjects, and those with secondary school and junior college or above accounting for 71.1% and 18.4%. The individual PM2.5 exposure concentration of 76 subjects during the study period was (58.7±53.7) μg/m[3]. DMM model showed that the subjects could be divided into four enterotypes, which were mainly driven by Bacteroides, Faecalibacterium, Lachnospiraceae, Prevotellaceae, and Ruminococcaceae. Linear mixed effects model showed that different lag periods of PM2.5 exposure were significantly associated with a lower gut α diversity index (P<0.05 after correction). Further analysis showed that PM2.5 exposure was significantly associated with changes in the abundances of Firmicutes (Megamonas, Blautia, Streptococcus, etc.) and Bacteroidetes (Alistipes) (P<0.05 after correction). Conclusion: Short-term PM2.5 exposure is significantly associated with a decrease in gut microbiome diversity and changes in the abundance of several species of Firmicutes and Bacteroidetes in the elderly. It is necessary to further explore the underlying mechanisms between PM2.5 exposure and the gut microbiome, so as to provide a scientific basis for promoting the intestinal health of the elderly.}, }
@article {pmid37198683, year = {2023}, author = {Cadar, AN and Martin, DE and Bartley, JM}, title = {Targeting the hallmarks of aging to improve influenza vaccine responses in older adults.}, journal = {Immunity &amp; ageing : I &amp; A}, volume = {20}, number = {1}, pages = {23}, pmid = {37198683}, issn = {1742-4933}, abstract = {Age-related declines in immune response pose a challenge in combating diseases later in life. Influenza (flu) infection remains a significant burden on older populations and often results in catastrophic disability in those who survive infection. Despite having vaccines designed specifically for older adults, the burden of flu remains high and overall flu vaccine efficacy remains inadequate in this population. Recent geroscience research has highlighted the utility in targeting biological aging to improve multiple age-related declines. Indeed, the response to vaccination is highly coordinated, and diminished responses in older adults are likely not due to a singular deficit, but rather a multitude of age-related declines. In this review we highlight deficits in the aged vaccine responses and potential geroscience guided approaches to overcome these deficits. More specifically, we propose that alternative vaccine platforms and interventions that target the hallmarks of aging, including inflammation, cellular senescence, microbiome disturbances, and mitochondrial dysfunction, may improve vaccine responses and overall immunological resilience in older adults. Elucidating novel interventions and approaches that enhance immunological protection from vaccination is crucial to minimize the disproportionate effect of flu and other infectious diseases on older adults.}, }
@article {pmid37198426, year = {2023}, author = {Benincà, E and Pinto, S and Cazelles, B and Fuentes, S and Shetty, S and Bogaards, JA}, title = {Wavelet clustering analysis as a tool for characterizing community structure in the human microbiome.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8042}, pmid = {37198426}, issn = {2045-2322}, abstract = {Human microbiome research is helped by the characterization of microbial networks, as these may reveal key microbes that can be targeted for beneficial health effects. Prevailing methods of microbial network characterization are based on measures of association, often applied to limited sampling points in time. Here, we demonstrate the potential of wavelet clustering, a technique that clusters time series based on similarities in their spectral characteristics. We illustrate this technique with synthetic time series and apply wavelet clustering to densely sampled human gut microbiome time series. We compare our results with hierarchical clustering based on temporal correlations in abundance, within and across individuals, and show that the cluster trees obtained by using either method are significantly different in terms of elements clustered together, branching structure and total branch length. By capitalizing on the dynamic nature of the human microbiome, wavelet clustering reveals community structures that remain obscured in correlation-based methods.}, }
@article {pmid37198262, year = {2023}, author = {Smith, CJ and Rendina, DN and Kingsbury, MA and Malacon, KE and Nguyen, DM and Tran, JJ and Devlin, BA and Raju, RM and Clark, MJ and Burgett, L and Zhang, JH and Cetinbas, M and Sadreyev, RI and Chen, K and Iyer, MS and Bilbo, SD}, title = {Microbial modulation via cross-fostering prevents the effects of pervasive environmental stressors on microglia and social behavior, but not the dopamine system.}, journal = {Molecular psychiatry}, volume = {}, number = {}, pages = {}, pmid = {37198262}, issn = {1476-5578}, abstract = {Environmental toxicant exposure, including air pollution, is increasing worldwide. However, toxicant exposures are not equitably distributed. Rather, low-income and minority communities bear the greatest burden, along with higher levels of psychosocial stress. Both air pollution and maternal stress during pregnancy have been linked to neurodevelopmental disorders such as autism, but biological mechanisms and targets for therapeutic intervention remain poorly understood. We demonstrate that combined prenatal exposure to air pollution (diesel exhaust particles, DEP) and maternal stress (MS) in mice induces social behavior deficits only in male offspring, in line with the male bias in autism. These behavioral deficits are accompanied by changes in microglial morphology and gene expression as well as decreased dopamine receptor expression and dopaminergic fiber input in the nucleus accumbens (NAc). Importantly, the gut-brain axis has been implicated in ASD, and both microglia and the dopamine system are sensitive to the composition of the gut microbiome. In line with this, we find that the composition of the gut microbiome and the structure of the intestinal epithelium are significantly shifted in DEP/MS-exposed males. Excitingly, both the DEP/MS-induced social deficits and microglial alterations in males are prevented by shifting the gut microbiome at birth via a cross-fostering procedure. However, while social deficits in DEP/MS males can be reversed by chemogenetic activation of dopamine neurons in the ventral tegmental area, modulation of the gut microbiome does not impact dopamine endpoints. These findings demonstrate male-specific changes in the gut-brain axis following DEP/MS and suggest that the gut microbiome is an important modulator of both social behavior and microglia.}, }
@article {pmid37198098, year = {2023}, author = {Hartmann, P and Lang, S and Schierwagen, R and Klein, S and Praktiknjo, M and Trebicka, J and Schnabl, B}, title = {Fecal cytolysin does not predict disease severity in acutely decompensated cirrhosis and acute-on-chronic liver failure.}, journal = {Hepatobiliary &amp; pancreatic diseases international : HBPD INT}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.hbpd.2023.05.003}, pmid = {37198098}, issn = {1499-3872}, abstract = {BACKGROUND: Cirrhosis with acute decompensation (AD) and acute-on-chronic liver failure (ACLF) are characterized by high morbidity and mortality. Cytolysin, a toxin from Enterococcus faecalis (E. faecalis), is associated with mortality in alcohol-associated hepatitis (AH). It is unclear whether cytolysin also contributes to disease severity in AD and ACLF.<br><br>METHODS: We studied the role of fecal cytolysin in 78 cirrhotic patients with AD/ACLF. Bacterial DNA from fecal samples was extracted and real-time quantitative polymerase chain reaction (PCR) was performed. The association between fecal cytolysin and liver disease severity in cirrhosis with AD or ACLF was analyzed.<br><br>RESULTS: Fecal cytolysin and E. faecalis abundance did not predict chronic liver failure (CLIF-C) AD and ACLF scores. Presence of fecal cytolysin was not associated with other liver disease markers, including Fibrosis-4 (FIB-4) index, 'Age, serum Bilirubin, INR, and serum Creatinine (ABIC)' score, Child-Pugh score, model for end-stage liver disease (MELD) nor MELD-Na scores in AD or ACLF patients.<br><br>CONCLUSIONS: Fecal cytolysin does not predict disease severity in AD and ACLF patients. The predictive value of fecal cytolysin positivity for mortality appears to be restricted to AH.}, }
@article {pmid37198061, year = {2023}, author = {Champagne-Jorgensen, K and Luong, T and Darby, T and Roach, DR}, title = {Immunogenicity of bacteriophages.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2023.04.008}, pmid = {37198061}, issn = {1878-4380}, abstract = {Hundreds of trillions of diverse bacteriophages (phages) peacefully thrive within and on the human body. However, whether and how phages influence their mammalian hosts is poorly understood. In this review, we explore current knowledge and present growing evidence that direct interactions between phages and mammalian cells often induce host inflammatory and antiviral immune responses. We show evidence that, like viruses of the eukaryotic host, phages are actively internalized by host cells and activate conserved viral detection receptors. This interaction often generates proinflammatory cytokine secretion and recruitment of adaptive immune programs. However, significant variability exists in phage-immune interactions, suggesting an important role for structural phage characteristics. The factors leading to the differential immunogenicity of phages remain largely unknown but are highly influenced by their human and bacterial hosts.}, }
@article {pmid37198015, year = {2023}, author = {Jubber, I and Ong, S and Bukavina, L and Black, PC and Compérat, E and Kamat, AM and Kiemeney, L and Lawrentschuk, N and Lerner, SP and Meeks, JJ and Moch, H and Necchi, A and Panebianco, V and Sridhar, SS and Znaor, A and Catto, JWF and Cumberbatch, MG}, title = {Epidemiology of Bladder Cancer in 2023: A Systematic Review of Risk Factors.}, journal = {European urology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.eururo.2023.03.029}, pmid = {37198015}, issn = {1873-7560}, abstract = {CONTEXT: Bladder cancer (BC) is common worldwide and poses a significant public health challenge. External risk factors and the wider exposome (totality of exposure from external and internal factors) contribute significantly to the development of BC. Therefore, establishing a clear understanding of these risk factors is the key to prevention.<br><br>OBJECTIVE: To perform an up-to-date systematic review of BC's epidemiology and external risk factors.<br><br>EVIDENCE ACQUISITION: Two reviewers (I.J. and S.O.) performed a systematic review using PubMed and Embase in January 2022 and updated it in September 2022. The search was restricted to 4 yr since our previous review in 2018.<br><br>EVIDENCE SYNTHESIS: Our search identified 5177 articles and a total of 349 full-text manuscripts. GLOBOCAN data from 2020 revealed an incidence of 573&#xa0;000 new BC cases and 213&#xa0;000 deaths worldwide in 2020. The 5-yr prevalence worldwide in 2020 was 1&#xa0;721&#xa0;000. Tobacco smoking and occupational exposures (aromatic amines and polycyclic aromatic hydrocarbons) are the most substantial risk factors. In addition, correlative evidence exists for several risk factors, including specific dietary factors, imbalanced microbiome, gene-environment risk factor interactions, diesel exhaust emission exposure, and pelvic radiotherapy.<br><br>CONCLUSIONS: We present a contemporary overview of the epidemiology of BC and the current evidence for BC risk factors. Smoking and specific occupational exposures are the most established risk factors. There is emerging evidence for specific dietary factors, imbalanced microbiome, gene-external risk factor interactions, diesel exhaust emission exposure, and pelvic radiotherapy. Further high-quality evidence is required to confirm initial findings and further understand cancer prevention.<br><br>PATIENT SUMMARY: Bladder cancer is common, and the most substantial risk factors are smoking and workplace exposure to suspected carcinogens. On-going research to identify avoidable risk factors could reduce the number of people who get bladder cancer.}, }
@article {pmid37197907, year = {2023}, author = {Kinross, JM}, title = {Microbiome is the key to preventing anastomotic leak in colorectal surgery.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2022-329281}, pmid = {37197907}, issn = {1468-3288}, }
@article {pmid37197624, year = {2023}, author = {Shah, H and Ng, TL}, title = {A narrative review from gut to lungs: non-small cell lung cancer and the gastrointestinal microbiome.}, journal = {Translational lung cancer research}, volume = {12}, number = {4}, pages = {909-926}, pmid = {37197624}, issn = {2218-6751}, abstract = {BACKGROUND AND OBJECTIVE: The gut microbiome has emerged as an important gateway to improving therapeutic outcomes in lung cancer, especially for immunotherapy. Our objective is to review the impact of the bidirectional relationship between the gut microbiome, lung cancer, and the immune system, and to identify areas of future research.<br><br>METHODS: We conducted a search on PubMed, EMBASE, and ClinicalTrials.gov using the search terms non-small cell lung cancer (NSCLC), gut microbiome, and microbiota until July 11, 2022. The authors screened resulting studies independently. Results were synthesized and presented descriptively.<br><br>KEY CONTENT AND FINDINGS: Sixty original published studies were identified from PubMed (n=24) and EMBASE (n=36), respectively. Twenty-five ongoing clinical studies were identified on ClinicalTrials.gov. Gut microbiota has been shown to influence tumorigenesis and modulate tumor immunity via local and neurohormonal mechanisms depending on the microbiome ecosystem that populates the gastrointestinal tract. Probiotics, antibiotics, and proton pump inhibitors (PPIs), amongst other medications, can impact gut microbiome health, leading either to improved or worsened therapeutic outcomes with immunotherapy. Most clinical studies assess the impact of the gut microbiome, but emerging data suggest microbiome composition in other host sites may be important.<br><br>CONCLUSIONS: A strong relationship exists between gut microbiome, oncogenesis, and anticancer immunity. Although the underlying mechanisms are poorly understood, immunotherapy outcomes seem to depend on host-related factors such as gut microbiome alpha diversity, relative abundance of microbial genera/taxa, and extrinsic factors such as prior or concurrent exposure to probiotics, antibiotics, and other microbiome-modifying drugs.}, }
@article {pmid37197442, year = {2023}, author = {Pinato, DJ and Li, X and Mishra-Kalyani, P and D'Alessio, A and Fulgenzi, CAM and Scheiner, B and Pinter, M and Wei, G and Schneider, J and Rivera, DR and Pazdur, R and Theoret, MR and Casak, S and Lemery, S and Fashoyin-Aje, L and Cortellini, A and Pelosof, L}, title = {Association between antibiotics and adverse oncological outcomes in patients receiving targeted or immune-based therapy for hepatocellular carcinoma.}, journal = {JHEP reports : innovation in hepatology}, volume = {5}, number = {6}, pages = {100747}, pmid = {37197442}, issn = {2589-5559}, abstract = {BACKGROUND &amp; AIMS: Immune checkpoint inhibitors (ICIs) alone or in combination with other ICIs or vascular endothelial growth factor pathway inhibitors are therapeutic options in unresectable/metastatic hepatocellular carcinoma (HCC). Whether antibiotic (ATB) exposure affects outcome remains unclear.<br><br>METHODS: This study retrospectively analysed an FDA database including 4,098 patients receiving ICI (n&#xa0;= 842) either as monotherapy (n&#xa0;= 258) or in combination (n&#xa0;= 584), tyrosine kinase inhibitor (TKI) (n&#xa0;= 1,968), vascular endothelial growth factor pathway inhibitors (n&#xa0;= 480), or placebo (n&#xa0;= 808) as part of nine international clinical trials. Exposure to ATB within 30 days before or after treatment initiation was correlated with overall survival (OS) and progression-free survival (PFS) across therapeutic modality before and after inverse probability of treatment weighting (IPTW).<br><br>RESULTS: Of 4,098 patients with unresectable/metastatic HCC, of which 39% were of hepatitis B aetiology and 21% were of hepatitis C aetiology, 83% were males with a median age of 64 years (range 18-88), a European Collaborative Oncology Group performance status of 0 (60%), and Child-Pugh A class (98%). Overall, ATB exposure (n&#xa0;= 620, 15%) was associated with shorter median PFS (3.6 months in ATB-exposed vs. 4.2 months; hazard ratio [HR] 1.29; 95% CI 1.22, 1.36) and OS (8.7 months in ATB-exposed vs. 10.6 months; HR 1.36; 95% CI 1.29, 1.43). In IPTW analyses, ATB was associated with shorter PFS in patients treated with ICI (HR 1.52; 95% CI 1.34, 1.73), TKI (HR 1.29; 95% CI 1.19, 1.39), and placebo (HR 1.23; 95% CI 1.11, 1.37). Similar results were observed in IPTW analyses of OS in patients treated with ICI (HR 1.22; 95% CI 1.08, 1.38), TKI (HR 1.40; 95% CI 1.30, 1.52), and placebo (HR 1.40; 95% CI 1.25, 1.57).<br><br>CONCLUSIONS: Unlike other malignancies where the detrimental effect of ATB may be more prominent in ICI recipients, ATB is associated with worse outcomes in this study across different therapies for HCC including placebo. Whether ATB is causally linked to worse outcomes through disruption of the gut-liver axis remains to be demonstrated in translational studies.<br><br>IMPACT AND IMPLICATIONS: A growing body of evidence suggests the host microbiome, frequently altered by antibiotic treatment, as an important outcome predictor in the context of immune checkpoint inhibitor therapy. In this study, we analysed the effects of early antibiotic exposure on outcomes in almost 4,100 patients with hepatocellular carcinoma treated within nine multicentre clinical trials. Interestingly, early exposure to antibiotic treatment was associated with worse outcomes not only in patients treated with immune checkpoint inhibitors but also in those treated with tyrosine kinase inhibitors and placebo. This is in contrast to data published in other malignancies, where the detrimental effect of antibiotic treatment may be more prominent in immune checkpoint inhibitor recipients, highlighting the uniqueness of hepatocellular carcinoma given the complex interplay between cirrhosis, cancer, risk of infection, and the pleiotropic effect of molecular therapies for this disease.}, }
@article {pmid37116651, year = {2023}, author = {Dar, SH and Maniya, MT and Merza, N and Musheer, A and Zahid, M and Ahmed, F and Shurjeel, Q and Qazi, S and Ahmed, A and Shah, H and Zafar, A and Iqbal, AZ and Khan, SF and Rizwan, T and Ligresti, R}, title = {The association of antibiotic exposure with new-onset inflammatory bowel disease: A systematic review and meta-analysis.}, journal = {Clinics and research in hepatology and gastroenterology}, volume = {47}, number = {6}, pages = {102129}, doi = {10.1016/j.clinre.2023.102129}, pmid = {37116651}, issn = {2210-741X}, abstract = {INTRODUCTION: The role of antibiotics in the development of inflammatory bowel disease (IBD) remains controversial, primarily due to conflicting data from individual studies. We conduct a systematic review and meta-analysis to study the effect of antibiotic exposure on IBD development.<br><br>METHODOLOGY: The MEDLINE and Cochrane CENTRAL databases were queried from their inception to April 2021 for published articles studying the association between antibiotic exposure and new-onset IBD. Our analysis was stratified by timing of antibiotic exposure - exposure in childhood and any lifetime exposure. Adjusted odds ratios (ORs) and corresponding 95% confidence intervals (CIs) from each study were pooled using a random-effects model.<br><br>RESULTS: 10 case-control studies and 2 cohort studies (N&#xa0;=&#xa0;29,880 IBD patients and N&#xa0;=&#xa0;715,548 controls) were included. Patients with Crohn's Disease (CD), compared with controls, were associated significantly with antibiotic exposure in childhood and any lifetime exposure to antibiotics (OR 1.52 [1.23-1.87]; p<0.00001). Patients with Ulcerative Colitis (UC), compared with controls, reported non-significant association with antibiotic exposure in childhood and any lifetime exposure. (OR 1.11 [0.93-1.33]; p&#xa0;=&#xa0;0.25) CONCLUSION: This meta-analysis suggests that exposure to antibiotics significantly increases the odds of developing CD and IBD. These findings re-emphasize the importance of cautious and judicious use of antibiotics.}, }
@article {pmid37197440, year = {2023}, author = {Dora, D and Ligeti, B and Kovacs, T and Revisnyei, P and Galffy, G and Dulka, E and Krizsán, D and Kalcsevszki, R and Megyesfalvi, Z and Dome, B and Weiss, GJ and Lohinai, Z}, title = {Non-small cell lung cancer patients treated with Anti-PD1 immunotherapy show distinct microbial signatures and metabolic pathways according to progression-free survival and PD-L1 status.}, journal = {Oncoimmunology}, volume = {12}, number = {1}, pages = {2204746}, doi = {10.1080/2162402X.2023.2204746}, pmid = {37197440}, issn = {2162-402X}, abstract = {Due to the high variance in response rates concerning anti-PD1 immunotherapy (IT), there is an unmet need to discover innovative biomarkers to predict immune checkpoint inhibitor (ICI)-efficacy. Our study included 62 Caucasian advanced-stage non-small cell lung cancer (NSCLC) patients treated with anti-PD1 ICI. Gut bacterial signatures were evaluated by metagenomic sequencing and correlated with progression-free survival (PFS), PD-L1 expression and other clinicopathological parameters. We confirmed the predictive role of PFS-related key bacteria with multivariate statistical models (Lasso- and Cox-regression) and validated on an additional patient cohort (n = 60). We find that alpha-diversity showed no significant difference in any comparison. However, there was a significant difference in beta-diversity between patients with long- (>6 months) vs. short (≤6 months) PFS and between chemotherapy (CHT)-treated vs. CHT-naive cases. Short PFS was associated with increased abundance of Firmicutes (F) and Actinobacteria phyla, whereas elevated abundance of Euryarchaeota was specific for low PD-L1 expression. F/Bacteroides (F/B) ratio was significantly increased in patients with short PFS. Multivariate analysis revealed an association between Alistipes shahii, Alistipes finegoldii, Barnesiella visceriola, and long PFS. In contrast, Streptococcus salivarius, Streptococcus vestibularis, and Bifidobacterium breve were associated with short PFS. Using Random Forest machine learning approach, we find that taxonomic profiles performed superiorly in predicting PFS (AUC = 0.74), while metabolic pathways including Amino Acid Synthesis and Fermentation were better predictors of PD-L1 expression (AUC = 0.87). We conclude that specific metagenomic features of the gut microbiome, including bacterial taxonomy and metabolic pathways might be suggestive of ICI efficacy and PD-L1 expression in NSCLC patients.}, }
@article {pmid37197270, year = {2023}, author = {Fratila, TD and Ismaiel, A and Dumitrascu, DL}, title = {Microbiome modulation in the prevention and management of colorectal cancer: a systematic review of clinical interventions.}, journal = {Medicine and pharmacy reports}, volume = {96}, number = {2}, pages = {131-145}, doi = {10.15386/mpr-2526}, pmid = {37197270}, issn = {2668-0572}, abstract = {INTRODUCTION: The role of probiotics/prebiotics in modulating the procarcinogenic effects of microbiota have been studied with inconclusive results. This systematic review aimed to identify the role of several studied interventions on the gut microbiota modulation in humans for the prevention and management of colorectal cancer (CRC).<br><br>METHODS: We conducted a systematic search using PubMed and Cochrane Central electronic databases, identifying clinical studies published within the last 20 years. We performed a qualitative analysis of eligible studies included in our review on each of the 4 investigated topics: CRC potential biomarkers, dietary interventions, probiotic administration in non-surgical and surgical patients, respectively.<br><br>RESULTS: A total of 54 studies involving healthy volunteers, in addition to colorectal adenoma and CRC patients were included in our qualitative synthesis. We were able to identify bacterial signatures of CRC including Fusobacterium nucleatum and Clostridium butyricum. Moreover, dietary supplementation with oligosaccharides or fibers increased short chain fatty acid-producing bacteria levels, thus inhibiting tumorigenesis. Furthermore, we have confirmed that Lactobacilli and Bifidobacterium intake modulates gut microbiota towards tumor suppression. We have also showed that probiotic intake around colectomy significantly reduces complications.<br><br>CONCLUSIONS: Bacterial metabolism is strongly linked with colonic carcinogenesis and influenced by diet. Probiotics and prebiotics can act as microbiota modulators, suppressing epithelial proliferation and reversing DNA toxicity. As adjuvants to surgery or chemotherapy, Lactobacilli and Bifidobacteria decrease complications. Improved outcomes in CRC patients can possibly be achieved through future research directed towards the benefits of bacterial agents as tumor suppressors or as treatment of oncological therapy resistance.}, }
@article {pmid37197229, year = {2023}, author = {Zhang, X and Wang, X and Zhao, H and Cao, R and Dang, Y and Yu, B}, title = {Imbalance of Microbacterial Diversity Is Associated with Functional Prognosis of Stroke.}, journal = {Neural plasticity}, volume = {2023}, number = {}, pages = {6297653}, doi = {10.1155/2023/6297653}, pmid = {37197229}, issn = {1687-5443}, abstract = {OBJECTIVES: There is mounting evidence to suggest that the pathophysiology of stroke is greatly influenced by the microbiota of the gut and its metabolites, in particular short-chain fatty acids (SCFAs). The primary purpose of the study was to evaluate whether the levels of SCFAs and the gut microbiota are altered in poststroke patients and to examine the relationship between these alterations and the physical condition, intestinal health, pain, or nutritional status of patients.<br><br>METHODS: Twenty stroke patients and twenty healthy controls were enrolled in the current study, and their demographics were matched. Gas chromatography was used to determine the fecal SCFAs, and 16S rRNA gene sequencing was used to evaluate their fecal microbiota. Microbial diversity and richness were examined using the diversity indices alpha and beta, and taxonomic analysis was utilized to determine group differences. The relationships between the gut microbiome and fecal SCFAs, discriminant bacteria, and poststroke clinical outcomes were analyzed.<br><br>RESULTS: Less community richness (ACE and Chao) was observed in the poststroke patients (P < 0.05), but the differences between the poststroke group and the healthy control group in terms of species diversity (Shannon and Simpson) were not statistically significant. The makeup of the poststroke gut microbiota was distinct from that of the control group, as evidenced by beta diversity. Then, the relative abundances of the taxa in the poststroke and control groups were compared in order to identify the specific microbiota changes. At the level of phylum, the poststroke subjects showed a significant increase in the relative abundances of Akkermansiaceae, Fusobacteriota, Desulfobacterota, Ruminococcaceae, and Oscillospirales and a particularly noticeable decrease in the relative abundance of Acidobacteriota compared to the control subjects (P < 0.05). In regard to SCFA concentrations, lower levels of fecal acetic acid (P = 0.001) and propionic acid (P = 0.049) were found in poststroke subjects. Agathobacter was highly correlated with acetic acid level (r = 0.473, P = 0.002), whereas Fusobacteria (r = -0.371, P = 0.018), Flavonifractor (r = -0.334, P = 0.034), Desulfovibrio (r = -0.362, P = 0.018), and Akkermansia (r = -0.321, P = 0.043) were negatively related to acetic acid levels. Additionally, the findings of the correlation analysis revealed that Akkermansia (r = -0.356, P = 0.024), Desulfovibrio (r = -0.316, P = 0.047), and Alloprevotella (r = -0.366, P = 0.020) were significantly negatively correlated with high-density lipoprotein cholesterol. In addition, the Neurogenic Bowel Dysfunction score (r = 0.495, P = 0.026), Barthel index (r = -0.531, P = 0.015), Fugl-Meyer Assessment score (r = -0.565, P = 0.009), Visual Analogue Scale score (r = 0.605, P = 0.005), and Brief Pain Inventory score (r = 0.507, P = 0.023) were significantly associated with alterations of distinctive gut microbiota.<br><br>CONCLUSIONS: Stroke generates extensive and substantial alterations in the gut microbiota and SCFAs, according to our findings. The differences of intestinal flora and lower fecal SCFA levels are closely related to the physical function, intestinal function, pain, or nutritional status of poststroke patients. Treatment strategies aimed at modulating the gut microbiota and SCFAs may have the potential to enhance the clinical results of patients.}, }
@article {pmid37197021, year = {2023}, author = {Chaudhari, HG and Prajapati, S and Wardah, ZH and Raol, G and Prajapati, V and Patel, R and Shati, AA and Alfaifi, MY and Elbehairi, SEI and Sayyed, RZ}, title = {Decoding the microbial universe with metagenomics: a brief insight.}, journal = {Frontiers in genetics}, volume = {14}, number = {}, pages = {1119740}, doi = {10.3389/fgene.2023.1119740}, pmid = {37197021}, issn = {1664-8021}, abstract = {A major part of any biological system on earth involves microorganisms, of which the majority are yet to be cultured. The conventional methods of culturing microbes have given fruitful outcomes yet have limitations. The curiosity for better understanding has led to the development of culture-independent molecular methods that help push aside the roadblocks of earlier methods. Metagenomics unifies the scientific community in search of a better understanding of the functioning of the ecosystem and its component organisms. This approach has opened a new paradigm in advanced research. It has brought to light the vast diversity and novelty among microbial communities and their genomes. This review focuses on the development of this field over time, the techniques and analysis of data generated through sequencing platforms, and its prominent interpretation and representation.}, }
@article {pmid37196943, year = {2023}, author = {Yu, Z and Lu, T and Qian, H}, title = {Pesticide interference and additional effects on plant microbiomes.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164149}, doi = {10.1016/j.scitotenv.2023.164149}, pmid = {37196943}, issn = {1879-1026}, abstract = {Pesticides are essential to modern human production activities, particularly those increasing global food production and quality; however, corresponding pesticide contamination is becoming more prominent. Plant microbiomes, containing different assemblages of microbial communities in the rhizosphere, endosphere, and phyllosphere, in addition to the mycorrhizal microbiome, substantially impact plant health and productivity. Therefore, the relationships among pesticides, plant microbiomes, and plant communities are important to evaluate the ecological safety of pesticides. To date, the majority of research efforts aimed at understanding the effects of pesticides on microbial communities have focused on single niche microbiomes. However, a comprehensive review of the effects of pesticides on microbial communities and co-occurrence patterns in different ecological niches is still lacking. This review fills this gap by providing an overview of the effects of pesticides on plant microbial communities across ecological niches. Specifically, we discuss the potential feedback and risks associated with these effects on plant health. Through a thorough examination of the available literature, we provide a comprehensive perspective of the impacts of pesticides on plant microbiomes, which may facilitate the development of effective strategies to mitigate these effects.}, }
@article {pmid37196884, year = {2023}, author = {Lehman, P and Cady, N and Ghimire, S and Shahi, SK and Shrode, RL and Lehmler, HJ and Mangalam, AK}, title = {Low-dose glyphosate exposure alters gut microbiota composition and modulates gut homeostasis.}, journal = {Environmental toxicology and pharmacology}, volume = {}, number = {}, pages = {104149}, doi = {10.1016/j.etap.2023.104149}, pmid = {37196884}, issn = {1872-7077}, abstract = {The widespread use of glyphosate, a broad-spectrum herbicide, has resulted in significant human exposure, and recent studies have challenged the notion that glyphosate is safe for humans. Although the link between disease states and glyphosate exposure is increasingly appreciated, the mechanistic links between glyphosate and its toxic effects on human health are poorly understood. Recent studies have suggested that glyphosate may cause toxicity through modulation of the gut microbiome, but evidence for glyphosate-induced gut dysbiosis and its effect on host physiology at doses approximating the U.S. Acceptable Daily Intake (ADI = 1.75mg/kg body weight) is limited. Here, utilizing shotgun metagenomic sequencing of fecal samples from C57BL/6J mice, we show that glyphosate exposure at doses approximating the U.S. ADI significantly impacts gut microbiota composition. These gut microbial alterations were associated with effects on gut homeostasis characterized by increased proinflammatory CD4[+]IL17A[+] T cells and Lipocalin-2, a known marker of intestinal inflammation. DATA AVAILABILITY: The shotgun metagenomic sequences are deposited in NCBI under BioProject PRJNA880821. All other data needed to evaluate the conclusions in the manuscript are present in the manuscript and/or the Supplementary Materials.}, }
@article {pmid37196816, year = {2023}, author = {Feng, L and Bao, T and Bai, L and Mu, X and Ta, N and Bao, M and Li, Y and Zhang, J and Fu, M and Chen, Y}, title = {Mongolian medicine formulae Ruda-6 alleviates indomethacin-induced gastric ulcer by regulating gut microbiome and serum metabolomics in rats.}, journal = {Journal of ethnopharmacology}, volume = {}, number = {}, pages = {116545}, doi = {10.1016/j.jep.2023.116545}, pmid = {37196816}, issn = {1872-7573}, abstract = {Ruda-6 (RD-6), a typical traditional Mongolian medicine formulae consisting of 6 herbs, has been traditionally used in treating gastric disorders. Even though it has been shown to protect against gastric ulcers (GU) in animal models, the gut microbiome and serum metabololite-related mechanisms that prevent GU are not well understood.<br><br>AIM OF THE STUDY: This study was conducted to evaluate the gastroprotective mechanism of RD-6 associated with the alteration of the gut microbiome and serum metabolic profiles in GU rats.<br><br>MATERIALS AND METHODS: RD-6 (0.27, 1.35 and 2.7&#x202f;g/kg) or ranitidine (40&#x202f;mg/kg) were orally administered in rats for three weeks before the induction of gastric ulcer using indomethacin (30&#x202f;mg/kg, single oral dose). The gastric ulcer index, ulcer area, H&amp;E staining, and the levels of TNF-&#x3b1;, iNOS, MPO and MDA were quantified to evaluate the ulcer inhibitory effects of RD-6. Then, 16S rRNA gene sequencing combined with LC-MS metabolic profiling was performed to investigate the effect of RD-6 on the gut microbiota and serum metabolites in rats. Moreover, a spearman analysis was used to calculate the correlation coefficient between the different microbiota and the metabolites.<br><br>RESULTS: RD-6 inhibited the gastric lesion damage caused by indomethacin in rats, decreased the ulcer index by 50.29% (p&#x202f;<&#x202f;0.05), reduced the levels of TNF-&#x3b1;, iNOS, MDA and MPO in gastric tissue. Additionally, RD-6 reshaped the diversity and microbial composition, and reversed the reduced bacteria including [Eubacterium]_xylanophilum group, Sellimonas, Desulfovibrio, and UCG-009, and the increased bacteria Aquamicrobium caused by indomethacin induction. Furthermore, RD-6 regulated the levels of metabolites including amino acids and organic acids, and these affected metabolites were involved in taurine and hypotaurine metabolism and tryptophan metabolism. Spearman analysis revealed that the perturbed gut microbiota were closely related to the changes in differential serum metabolites.<br><br>CONCLUSION: In view of the 16S rRNA gene sequencing and LC-MS metabolic results, the present study suggests the mechanism of RD-6 ameliorating GU via modulating intestinal microbiota and their metabolites.}, }
@article {pmid37196700, year = {2023}, author = {Luo, G and K M Maitz, P and Wang, Y}, title = {Role of microbiome, microenvironment and novel drug delivery system in the wound healing.}, journal = {Advanced drug delivery reviews}, volume = {}, number = {}, pages = {114873}, doi = {10.1016/j.addr.2023.114873}, pmid = {37196700}, issn = {1872-8294}, }
@article {pmid37196633, year = {2023}, author = {Yadav, J and Liang, T and Qin, T and Nathan, N and Schwenger, KJP and Pickel, L and Xie, L and Lei, H and Winer, DA and Maughan, H and Robertson, SJ and Woo, M and Lou, W and Banks, K and Jackson, T and Okrainec, A and Hota, SS and Poutanen, SM and Sung, HK and Allard, JP and Philpott, DJ and Gaisano, HY}, title = {Gut microbiome modified by bariatric surgery improves insulin sensitivity and correlates with increased brown fat activity and energy expenditure.}, journal = {Cell reports. Medicine}, volume = {4}, number = {5}, pages = {101051}, doi = {10.1016/j.xcrm.2023.101051}, pmid = {37196633}, issn = {2666-3791}, abstract = {Alterations in the microbiome correlate with improved metabolism in patients following bariatric surgery. While fecal microbiota transplantation (FMT) from obese patients into germ-free (GF) mice has suggested a significant role of the gut microbiome in metabolic improvements following bariatric surgery, causality remains to be confirmed. Here, we perform paired FMT from the same obese patients (BMI > 40; four patients), pre- and 1 or 6 months post-Roux-en-Y gastric bypass (RYGB) surgery, into Western diet-fed GF mice. Mice colonized by FMT from patients' post-surgery stool exhibit significant changes in microbiota composition and metabolomic profiles and, most importantly, improved insulin sensitivity compared with pre-RYGB FMT mice. Mechanistically, mice harboring the post-RYGB microbiome show increased brown fat mass and activity and exhibit increased energy expenditure. Moreover, improvements in immune homeostasis within the white adipose tissue are also observed. Altogether, these findings point to a direct role for the gut microbiome in mediating improved metabolic health post-RYGB surgery.}, }
@article {pmid37196578, year = {2023}, author = {Bach, A and Elcoso, G and Escartín, M and Spengler, K and Jouve, A}, title = {Modulation of milking performance, methane emissions, and rumen microbiome on dairy cows by dietary supplementation of a blend of essential oils.}, journal = {Animal : an international journal of animal bioscience}, volume = {17}, number = {6}, pages = {100825}, doi = {10.1016/j.animal.2023.100825}, pmid = {37196578}, issn = {1751-732X}, abstract = {Cattle represent a high contribution of the livestock's greenhouse gas emissions, mainly in the form of methane. Essential oils are a group of plant secondary metabolites obtained from volatile fractions of plants that have been shown to exert changes in the rumen fermentation and may alter feed efficiency and to reduce methane production. The objective of this study was to investigate the effect on rumen microbial population, CH4 emissions and milking performance of a mixture of essential oils (Agolin Ruminant, Switzerland) incorporated daily in the ration of dairy cattle. Forty Holstein cows (644 ± 63.5 kg of BW producing 41.2 ± 6.44 kg/d of milk with 190 ± 28.3 DIM) were divided into two treatments (n = 20) for 13 wk and housed in a single pen equipped with electronic feeding gates to control access to feed and monitor individual DM intake (DMI) on a daily basis. Treatments consisted of no supplementation (Control) or supplementation of 1 g/d of a blend of essential oils (BEOs) fed in the TMR. Individual milk production was recorded using electronic milk meters on a daily basis. Methane emissions were recorded using sniffers at the exit of the milking parlour. At day 64 of the study, a sample of rumen fluid was collected from 12 cows per treatment after the morning feeding using a stomach tube. There were no differences in DMI, milk yield, or milk composition between the two treatments. However, cows on BEO exhaled less CH4 (444 ± 12.5 l/d) than cows on Control (479 ± 12.5 l/d), and exhaled less (P < 0.05) CH4/kg of DM consumed (17.6 vs 20.1 ± 0.53 l/kg, respectively) from the first week of study, with no interaction with time, which suggests a fast action of BEO of CH4 emissions. Rumen relative abundance of Entodonium increased, and those of Fusobacteria, Chytridiomycota, Epidinium, and Mogibacterium decreased in BEO compared with Control cows. Supplementing 1 g/d of BEO reduces CH4 emissions on absolute terms (l/d) and diminishes the amount of CH4 produced by unit of DM consumed by cows relatively soon after the first supplementation, and the effect is sustained over time without impacting intake or milking performance.}, }
@article {pmid37196563, year = {2023}, author = {Herrera, BS and Henz, SL and Dua, S and Martin, L and Teles, RP and Patel, M and Teles, FRF}, title = {Pursuing new periodontal pathogens with an improved RNA-oligonucleotide quantification technique (ROQT).}, journal = {Archives of oral biology}, volume = {152}, number = {}, pages = {105721}, doi = {10.1016/j.archoralbio.2023.105721}, pmid = {37196563}, issn = {1879-1506}, abstract = {OBJECTIVE: The aim of this study was to optimize the sensitivity, specificity and cost-effectiveness of the RNA-Oligonucleotide Quantification Technique (ROQT) in order to identify periodontal pathogens that remain unrecognized or uncultured in the oral microbiome.<br><br>DESIGN: Total nucleic acids (TNA) were extracted from subgingival biofilm samples using an automated process. RNA, DNA and Locked Nucleic Acid (LNA) digoxigenin-labeled oligonucleotide probes targeting 5 cultivated/named species and 16 uncultivated or unnamed bacterial taxa were synthesized. Probe specificity was determined by targeting 96 oral bacterial species; sensitivity was assessed using serial dilutions of reference bacterial strains. Different stringency temperatures were compared and new standards were tested. The tested conditions were evaluated analyzing samples from periodontally healthy individuals, and patients with moderate or severe periodontitis.<br><br>RESULTS: The automated extraction method at 63&#x2070;C along with LNA-oligunucleotides probes, and use of reverse RNA sequences for standards yielded stronger signals without cross-reactions. In the pilot clinical study, the most commonly detected uncultivated/unrecognized species were Selenomonas sp. HMT 134, Prevotella sp. HMT 306, Desulfobulbus sp. HMT 041, Synergistetes sp. HMT 360 and Bacteroidetes HMT 274. In the cultivated segment of the microbiota, the most abundant taxa were T. forsythia HMT 613 and Fretibacterium fastidiosum (formerly Synergistetes) HMT 363.<br><br>CONCLUSIONS: In general, samples from severe patients had the greatest levels of organisms. Classic (T. forsythia, P. gingivalis) and newly proposed (F. alocis and Desulfobulbus sp. HMT 041) pathogens were present in greater amounts in samples from severe periodontitis sites, followed by moderate periodontitis sites.}, }
@article {pmid37196542, year = {2023}, author = {Petakh, P and Oksenych, V and Kamyshnyi, A}, title = {The F/B ratio as a biomarker for inflammation in COVID-19 and T2D: Impact of metformin.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {163}, number = {}, pages = {114892}, doi = {10.1016/j.biopha.2023.114892}, pmid = {37196542}, issn = {1950-6007}, abstract = {The pandemic of COVID-19 has highlighted the intricate relationship between gut microbiome and overall health. Recent studies have shown that the Firmicutes/Bacteroidetes ratio in the gut microbiome may be linked to various diseases including COVID-19 and type 2 diabetes (T2D). Understanding the link between gut microbiome and these diseases is essential for developing strategies for prevention and treatment. In this study, 115 participants were recruited and divided into three groups: 1st group: T2D patients and healthy controls, 2nd group: COVID-19 patients with and without T2D, 3rd group: T2D patients with COVID-19 treated with or without metformin. Gut microbial composition at the phylum level was assessed using qRT-PCR with universal primers targeting the bacterial 16 S rRNA gene and specific primers for Firmicutes and Bacteroidetes. Data was analyzed using one-way ANOVA, logistic regression, and Spearman's rank correlation coefficient. The study found that the ratio of Firmicutes to Bacteroidetes (F/B) was higher in patients with both T2D and COVID-19 compared to those with only T2D or COVID-19. Additionally, the F/B ratio was positively correlated with C-reactive protein (CRP) in T2D and COVID-19 patients. The study also suggests that metformin treatment may affect this correlation. Logistic regression analysis showed that the F/B ratio was significantly associated with CRP. These findings suggest that the F/B ratio may be a potential biomarker for inflammation in T2D and COVID-19 patients and metformin treatment may have an effect on the correlation between F/B and CRP levels.}, }
@article {pmid37196360, year = {2023}, author = {Moufarrej, MN and Bianchi, DW and Shaw, GM and Stevenson, DK and Quake, SR}, title = {Noninvasive Prenatal Testing Using Circulating DNA and RNA: Advances, Challenges, and Possibilities.}, journal = {Annual review of biomedical data science}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-biodatasci-020722-094144}, pmid = {37196360}, issn = {2574-3414}, abstract = {Prenatal screening using sequencing of circulating cell-free DNA has transformed obstetric care over the past decade and significantly reduced the number of invasive diagnostic procedures like amniocentesis for genetic disorders. Nonetheless, emergency care remains the only option for complications like preeclampsia and preterm birth, two of the most prevalent obstetrical syndromes. Advances in noninvasive prenatal testing expand the scope of precision medicine in obstetric care. In this review, we discuss advances, challenges, and possibilities toward the goal of providing proactive, personalized prenatal care. The highlighted advances focus mainly on cell-free nucleic acids; however, we also review research that uses signals from metabolomics, proteomics, intact cells, and the microbiome. We discuss ethical challenges in providing care. Finally, we look to future possibilities, including redefining disease taxonomy and moving from biomarker correlation to biological causation. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 6 is August 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, }
@article {pmid37196317, year = {2023}, author = {Luo, J and Tao, Q and Jupa, R and Liu, Y and Wu, K and Song, Y and Li, J and Huang, Y and Zou, L and Liang, Y and Li, T}, title = {Correction to "Role of Vertical Transmission of Shoot Endophytes in Root-Associated Microbiome Assembly and Heavy Metal Hyperaccumulation in Sedum alfredii".}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c02456}, pmid = {37196317}, issn = {1520-5851}, }
@article {pmid37196066, year = {2023}, author = {Anderson, ST and Meng, H and Brooks, TG and Tang, SY and Lordan, R and Sengupta, A and Nayak, S and Mřela, A and Sarantopoulou, D and Lahens, NF and Weljie, A and Grant, GR and Bushman, FD and FitzGerald, GA}, title = {Sexual dimorphism in the response to chronic circadian misalignment on a high-fat diet.}, journal = {Science translational medicine}, volume = {15}, number = {696}, pages = {eabo2022}, doi = {10.1126/scitranslmed.abo2022}, pmid = {37196066}, issn = {1946-6242}, abstract = {Longitudinal studies associate shiftwork with cardiometabolic disorders but do not establish causation or elucidate mechanisms of disease. We developed a mouse model based on shiftwork schedules to study circadian misalignment in both sexes. Behavioral and transcriptional rhythmicity were preserved in female mice despite exposure to misalignment. Females were protected from the cardiometabolic impact of circadian misalignment on a high-fat diet seen in males. The liver transcriptome and proteome revealed discordant pathway perturbations between the sexes. Tissue-level changes were accompanied by gut microbiome dysbiosis only in male mice, biasing toward increased potential for diabetogenic branched chain amino acid production. Antibiotic ablation of the gut microbiota diminished the impact of misalignment. In the United Kingdom Biobank, females showed stronger circadian rhythmicity in activity and a lower incidence of metabolic syndrome than males among job-matched shiftworkers. Thus, we show that female mice are more resilient than males to chronic circadian misalignment and that these differences are conserved in humans.}, }
@article {pmid37196005, year = {2023}, author = {Campbell, AC and Fei, T and Baik, JE and Park, HJ and Shin, J and Kuonqui, K and Brown, S and Sarker, A and Kataru, RP and Mehrara, BJ}, title = {Skin microbiome alterations in upper extremity secondary lymphedema.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0283609}, doi = {10.1371/journal.pone.0283609}, pmid = {37196005}, issn = {1932-6203}, abstract = {Lymphedema is a chronic condition that commonly occur from lymphatic injury following surgical resection of solid malignancies. While many studies have centered on the molecular and immune pathways that perpetuate lymphatic dysfunction, the role of the skin microbiome in lymphedema development remains unclear. In this study, skin swabs collected from normal and lymphedema forearms of 30 patients with unilateral upper extremity lymphedema were analyzed by 16S ribosomal RNA sequencing. Statistical models for microbiome data were utilized to correlate clinical variables with microbial profiles. Overall, 872 bacterial taxa were identified. There were no significant differences in microbial alpha diversity of the colonizing bacteria between normal and lymphedema skin samples (p = 0.25). Notably, for patients without a history of infection, a one-fold change in relative limb volume was significantly associated with a 0.58-unit increase in Bray-Curtis microbial distance between paired limbs (95%CI = 0.11,1.05, p = 0.02). Additionally, several genera, including Propionibacterium and Streptococcus, demonstrated high variability between paired samples. In summary, we demonstrate high compositional heterogeneity in the skin microbiome in upper extremity secondary lymphedema, supporting future studies into the role of host-microbe interactions on lymphedema pathophysiology.}, }
@article {pmid37195998, year = {2023}, author = {Dai, H and Hou, T and Wang, Q and Hou, Y and Wang, T and Zheng, J and Lin, H and Zhao, Z and Li, M and Wang, S and Zhang, D and Dai, M and Zheng, R and Lu, J and Xu, Y and Chen, Y and Ning, G and Wang, W and Bi, Y and Xu, M}, title = {Causal relationships between the gut microbiome, blood lipids, and heart failure: a Mendelian randomization analysis.}, journal = {European journal of preventive cardiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/eurjpc/zwad171}, pmid = {37195998}, issn = {2047-4881}, abstract = {BACKGROUND: Studies have linked gut microbiome and heart failure (HF). However, their causal relationships and potential mediating factors have not been well defined.<br><br>AIMS: To investigate the causal relationships between the gut microbiome and HF and the mediating effect of potential blood lipids by using genetics.<br><br>METHOD: We performed a bidirectional and mediation Mendelian randomization (MR) study using summary statistics from the genome-wide association studies of gut microbial taxa (Dutch Microbiome Project, n&#x2009;=&#x2009;7,738), blood lipids (UK Biobank, n&#x2009;=&#x2009;115,078), and a meta-analysis of HF (115,150 cases and 1,550,331 controls). We applied the inverse-variance weighted estimation method as the primary method, with several other estimators as complementary methods. The multivariable MR approach based on Bayesian model averaging (MR-BMA) was used to prioritize the most likely causal lipids.<br><br>RESULTS: Six microbial taxa are suggestively associated with HF causally. The most significant taxon was the species Bacteroides dorei (odds ratio&#x2009;=&#x2009;1.059, 95% confidence interval [CI]&#x2009;=&#x2009;1.022 - 1.097, P value&#x2009;=&#x2009;0.0017). The MR-BMA analysis showed that apolipoprotein B (ApoB) was the most likely causal lipid for HF (the marginal inclusion probability&#x2009;=&#x2009;0.717, P value&#x2009;=&#x2009;0.005). The mediation MR analysis showed that ApoB mediated the causal effects of species Bacteroides dorei on HF (proportion mediated&#x2009;=&#x2009;10.1%, 95% CI&#x2009;=&#x2009;0.2% - 21.6%, P value&#x2009;=&#x2009;0.031).<br><br>CONCLUSION: The study suggested a causal relationship between specific gut microbial taxa and HF and that ApoB might mediate this relationship as the primary lipid determinant of HF.}, }
@article {pmid37195935, year = {2023}, author = {Ji, X and Li, R and Hu, X and Tian, Y and Liu, L and Zhang, C and Xu, L and Chen, Y and Xie, H and Mao, L and Cai, T and Li, W}, title = {Construction of model animals to explore intestinal microbiome for detection of breast cancer.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0280971}, doi = {10.1371/journal.pone.0280971}, pmid = {37195935}, issn = {1932-6203}, abstract = {Breast cancer ranks first among female cancers and has become a major public health problem in the current society. More studies indicated that these cancers are related to the change in the gut microbiome that can cause metabolic and immune system disorders in the body. However, there are few studies on the changes in gut microbiome caused by the onset of breast cancer, and the relationship between breast cancer and gut microbiome needs to be further clarified. In this study, we inoculated 4T1 breast cancer cells to induce breast cancer tumorigenesis in mice and collected their feces samples at different stages during this process. These intestinal florae were analyzed using 16S rRNA gene amplicon sequencing, and the results showed that at the phylum level, the ratio of Firmicutes/Bacteroidetes decreased with the development of the tumor; at the family level, the intestinal microbiome had obvious variations of Lachnospiraceae, Bacteroidaceae, Erysipelotrichaceae, etc. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and COG annotation demonstrated that decreased abundance of cancer-related signaling pathways. This study elucidated the relationship between breast cancer and intestinal microbiome, and the research results can be used as an important biomarker for the diagnosis of breast cancer.}, }
@article {pmid37195907, year = {2023}, author = {Kinskey, JC and Huda, TI and Gozlan, EC and Quach, JU and Arturo, JF and Chobrutskiy, A and Chobrutskiy, BI and Blanck, G}, title = {The presence of intratumoral Porphyromonas gingivalis correlates with a previously defined pancreatic adenocarcinoma, immune cell expression phenotype and with tumor resident, adaptive immune receptor features.}, journal = {Carcinogenesis}, volume = {}, number = {}, pages = {}, doi = {10.1093/carcin/bgad033}, pmid = {37195907}, issn = {1460-2180}, abstract = {The association between pancreatic adenocarcinoma (PAAD) and the pancreatic microbiome is not fully understood, although bacteria may decrease the effectiveness of chemotherapy and lead to anti-apoptotic, pro-inflammatory-microenvironments. To better understand the relationship between the PAAD microbiome and the microenvironment, we identified Porphyromonas gingivalis-positive PAAD samples and found a strong association between intratumoral Porphyromonas gingivalis and: (a) an immune cell gene expression phenotype previously defined by others as gene program 7; and (b) recovery of immunoglobulin recombination, sequencing reads. We applied a novel chemical complementarity scoring algorithm, suitable for a big data setting, and determined that the previously established, Porphyromonas gingivalis antigen, rpgB had a reduced chemical complementarity with T-cell receptor (TCR) complementarity-determining region-3 amino acid sequences recovered from PAAD samples with Porphyromonas gingivalis in comparison to TCR-rpgB chemical complementarity represented by the PAAD samples that lacked Porphyromonas gingivalis. This finding strengthens the existing body of evidence correlating Pophyromonas gingivalis with PAAD, which may have implications for treatment and prognosis of patients. Furthermore, demonstrating the correlation of Pophryomonas gingivalis and gene program 7 raises the question of whether Pophryomonas gingivalis infection is responsible for the gene program 7 subdivision of PAAD?}, }
@article {pmid37195736, year = {2023}, author = {Zhu, JJ and Liu, HY and Yang, LJ and Fang, Z and Fu, R and Chen, JB and Liu, S and Fei, BY}, title = {Anti-tumour effect of Huangqin Decoction on colorectal cancer mice through microbial butyrate mediated PI3K/Akt pathway suppression.}, journal = {Journal of medical microbiology}, volume = {72}, number = {5}, pages = {}, doi = {10.1099/jmm.0.001692}, pmid = {37195736}, issn = {1473-5644}, abstract = {Introduction. Huangqin Decoction (HQD), a Chinese herbal formula, is widely used for various diseases, including colorectal cancer (CRC).Hypothesis/Gap Statement. We proposed that microbial butyrate mediated PI3K/Akt pathway suppression might involve the anti-cancer effect of HQD.Aim. This study aimed to evaluate the potential mechanism of HQD against CRC.Methodology. An azoxymethane plus dextran sulphate sodium induced CRC mouse model was used, and the intestinal flora and faecal short-chain fatty acid changes were detected, respectively, after HQD administration with 16S rRNA sequencing and gas chromatography coupled with mass spectrometry. Disease activity index, colon length and levels of inflammatory cytokines were measured to evaluate the effect of HQD on intestinal inflammation. Tumour size, number and histopathology were assessed to reflect the impact of HQD on tumour burden. Apoptosis and PI3K/Akt pathway activity were measured by TUNEL staining and Western-blotting. In vitro, the effects of sodium butyrate (NaB) on the viability of CRC cell lines were detected by the Cell-counting Kit-8. The apoptotic cells were determined by TUNEL staining. Cell migration and invasion were assessed by wound healing assay and Transwell assay, respectively. Western-blotting and immunofluorescent staining were used to test the activity of PI3K/Akt pathway.Results. Animal study showed that HQD could improve the gut dysbiosis, increase the abundance of Clostridium and the level of faecal butyric acid. Then, we found that HQD could attenuate colitis, reduce tumour burden, promote cell apoptosis and suppress PI3K/Akt pathway activity in CRC mice. In vitro experiment revealed that NaB treatment could inhibit cell growth, migration and invasion in CRC cell lines. Additionally, NaB enhanced cellular apoptosis, and reduced phosphorylated PI3K and Akt expressions. Interestingly, addition of 740Y-P, an agonist of PI3K, reversed the NaB effects on CRC cells.Conclusion. Overall, in this study, we revealed that HQD could induce apoptosis through microbial butyrate mediated PI3K/Akt inhibition and perform anti-CRC activity.}, }
@article {pmid37195730, year = {2023}, author = {Tanwar, AS and Shruptha, P and Jnana, A and Brand, A and Ballal, M and Satyamoorthy, K and Murali, TS}, title = {Emerging Pathogens in Planetary Health and Lessons from Comparative Genome Analyses of Three Clostridia Species.}, journal = {Omics : a journal of integrative biology}, volume = {}, number = {}, pages = {}, doi = {10.1089/omi.2023.0034}, pmid = {37195730}, issn = {1557-8100}, abstract = {Clostridioides difficile (CD) is a major planetary health burden. A Gram-positive opportunistic pathogen, CD, colonizes the large intestine and is implicated in sepsis, pseudomembranous colitis, and colorectal cancer. C. difficile infection typically following antibiotic exposure results in dysbiosis of the gut microbiome, and is one of the leading causes of diarrhea in the elderly population. While several studies have focused on the toxigenic strains of CD, gut commensals such as Clostridium butyricum (CB) and Clostridium tertium (CT) could harbor toxin/virulence genes, and thus pose a threat to human health. In this study, we sequenced and characterized three isolates, namely, CT (MALS001), CB (MALS002), and CD (MALS003) for their antimicrobial, cytotoxic, antiproliferative, genomic, and proteomic profiles. Although in vitro cytotoxic and antiproliferative potential were observed predominantly in CD MALS003, genome analysis revealed pathogenic potential of CB MALS002 and CT MALS001. Pangenome analysis revealed the presence of several accessory genes typically involved in fitness, virulence, and resistance characteristics in the core genomes of sequenced strains. The presence of an array of virulence and antimicrobial resistance genes in CB MALS002 and CT MALS001 suggests their potential role as emerging pathogens with significant impact on planetary health.}, }
@article {pmid37195254, year = {2023}, author = {Free, T}, title = {Long-read sequencing for the metagenomic analysis of microbiomes.}, journal = {BioTechniques}, volume = {74}, number = {4}, pages = {153-155}, doi = {10.2144/btn-2023-0028}, pmid = {37195254}, issn = {1940-9818}, abstract = {One technology, long-read sequencing, and one research field, microbiome studies, have risen to prominence over the last decade. But how can one be used in the other? What changes are being wrought? And what limitations remain? [Formula: see text].}, }
@article {pmid37195192, year = {2023}, author = {Wang, J and Pan, Z and Yu, J and Zhang, Z and Li, YZ}, title = {Global assembly of microbial communities.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0128922}, doi = {10.1128/msystems.01289-22}, pmid = {37195192}, issn = {2379-5077}, abstract = {Different habitats harbor different microbial communities with elusive assembly mechanisms. This study comprehensively investigated the global assembly mechanisms of microbial communities and effects of community-internal influencing factors using the Earth Microbiome Project (EMP) data set. We found that deterministic and stochastic processes contribute approximately equally to global microbial community assembly, and, specifically, deterministic processes generally play a major role in free-living and plant-associated (but not plant corpus) environments, while stochastic processes are the major contributor in animal-associated environments. In contrast with the assembly of microorganisms, the assembly of functional genes, predicted from PICRUSt, is mainly attributed to deterministic processes in all microbial communities. The sink and source microbial communities are normally assembled using similar mechanisms, and the core microorganisms are specific to different environment types. On a global scale, deterministic processes are positively related to the community alpha diversity, microbial interaction degree and bacterial predatory-specific gene abundance. Our analysis provides a panoramic picture and regularities of global and environment-typical microbial community assemblies.}, }
@article {pmid37195186, year = {2023}, author = {Byun, H and Brockett, MR and Pu, Q and Hrycko, AJ and Beld, J and Zhu, J}, title = {An Intestinal Bacillus velezensis Isolate Displays Broad-Spectrum Antibacterial Activity and Prevents Infection of Both Gram-Positive and Gram-Negative Pathogens In Vivo.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0013323}, doi = {10.1128/jb.00133-23}, pmid = {37195186}, issn = {1098-5530}, abstract = {The increasing prevalence of drug-resistant bacteria has significantly diminished the effectiveness of antibiotics in clinical settings, leading to the emergence of untreatable bacterial infections. To address this public health challenge, the gut microbiome represents a promising source of novel antimicrobial therapeutics. In this study, we screened mouse intestinal isolates for growth inhibitory activity against the human enteric pathogen Vibrio cholerae and identified a strain of spore-forming Bacillus velezensis, named BVM7, that produced a potent antibiotic with activity against V. cholerae and a broad spectrum of enteric and opportunistic pathogens. Characterization of the antimicrobial compounds produced by BVM7 revealed that they were primarily secreted antimicrobial peptides (AMPs) produced during stationary-phase growth. Furthermore, our results showed that introducing either BVM7 vegetative cells or spores into mice precolonized with V. cholerae or Enterococcus faecalis significantly reduced the burden of infection. Interestingly, we also observed that BVM7 was sensitive to a group of Lactobacillus probiotic strains and that inoculation of Lactobacilli could eliminate BVM7 and potentially restore the native gut microbiome. These findings highlight the potential of bacteria from the gut microbiome as a source for novel antimicrobial compounds and a tool for managing bacterial infections by in situ bio-delivery of multiple AMPs. IMPORTANCE The rise of antibiotic-resistant pathogens poses a challenge to public health. The gut microbiome presents a promising source of new antimicrobials and treatments. By screening murine gut commensals, we found a spore-forming Bacillus velezensis strain, BVM7, that exhibited antimicrobial activity toward a wide array of enteric and opportunistic bacterial pathogens. In addition to showing that this killing effect occurred through the action of secreted antimicrobial peptides (AMPs), we demonstrate that BVM7 vegetative cells and spores can be used to treat infections of both Gram-positive and Gram-negative pathogens in vivo. By expanding our knowledge of the antimicrobial properties of bacteria in the gut microbiome, we hope to contribute insights for developing novel drugs and therapeutic interventions.}, }
@article {pmid37195176, year = {2023}, author = {Xie, P and Yang, S and Liu, X and Zhang, T and Zhao, X and Wen, T and Zhang, J and Xue, C and Shen, Q and Yuan, J}, title = {Learning from Seed Microbes: Trichoderma Coating Intervenes in Rhizosphere Microbiome Assembly.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0309722}, doi = {10.1128/spectrum.03097-22}, pmid = {37195176}, issn = {2165-0497}, abstract = {Seed-associated microbiomes can impact the later colonization of a plant rhizosphere microbiome. However, there remains little insight into the underlying mechanisms concerning how alterations in the composition of the seed microbiome may intervene in the assembly of a rhizosphere microbiome. In this study, the fungus Trichoderma guizhouense NJAU4742 was introduced to both maize and watermelon seed microbiomes by seed coating. Application was found to significantly promote seed germination and improve plant growth and rhizosphere soil quality. The activities of acid phosphatase, cellulase, peroxidase, sucrase, and α-glucosidase increased significantly in two crops. The introduction of Trichoderma guizhouense NJAU4742 also led to a decrease in the occurrence of disease. Coating with T. guizhouense NJAU4742 did not alter the alpha diversities of the bacterial and fungal communities but formed a key network module that contained both Trichoderma and Mortierella. This key network module comprised of these potentially beneficial microorganisms was positively linked with the belowground biomass and activities of rhizosphere soil enzymes but negatively correlated with disease incidence. Overall, this study provides insights into plant growth promotion and plant health maintenance via seed coating in order to influence the rhizosphere microbiome. IMPORTANCE Seed-associated microbiomes can impact the rhizosphere microbiome assembly and function display. However, there remains little insight into the underlying mechanisms concerning how alterations in the composition of the seed microbiome with the beneficial microbes may intervene in the assembly of a rhizosphere microbiome. Here, we introduced T. guizhouense NJAU4742 to the seed microbiome by seed coating. This introduction led to a decrease in the occurrence of disease and an increase in plant growth; furthermore, it formed a key network module that contained both Trichoderma and Mortierella. Our study provides insights into plant growth promotion and plant health maintenance via seed coating in order to