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A wide variety of human diseases are associated with loss of microbial diversity in the human gut, inspiring a great interest in the diagnostic or therapeutic potential of the microbiota. However, the ecological forces that drive diversity reduction in disease states remain unclear, rendering it difficult to ascertain the role of the microbiota in disease emergence or severity. One hypothesis to explain this phenomenon is that microbial diversity is diminished as disease states select for microbial populations that are more fit to survive environmental stress caused by inflammation or other host factors. Here, we tested this hypothesis on a large scale, by developing a software framework to quantify the enrichment of microbial metabolisms in complex metagenomes as a function of microbial diversity. We applied this framework to over 400 gut metagenomes from individuals who are healthy or diagnosed with inflammatory bowel disease (IBD). We found that high metabolic independence (HMI) is a distinguishing characteristic of microbial communities associated with individuals diagnosed with IBD. A classifier we trained using the normalized copy numbers of 33 HMI-associated metabolic modules not only distinguished states of health versus IBD, but also tracked the recovery of the gut microbiome following antibiotic treatment, suggesting that HMI is a hallmark of microbial communities in stressed gut environments.

Background: The sodium-glucose cotransporter type 2 inhibitor dapagliflozin reduces the risk of progressive kidney disease and cardiovascular events in patients with chronic kidney disease, with and without type 2 diabetes. Whether its effects are uniform across the spectrum of age and among men and women is unknown., Objective: We performed a pre-specified analysis in DAPA-CKD to evaluate efficacy and safety of dapagliflozin according to baseline age and sex., Design: Prospective randomized placebo-controlled trial., Participants: A total of 4304 adults with chronic kidney disease (estimated glomerular filtration rate (eGFR) 25-75 mL/min/1.73 m 2 ; urinary albumin-to-creatinine ratio 200-5000 mg/g) with and without type 2 diabetes., Intervention: Dapagliflozin 10 mg versus placebo once daily., Main Measures: Primary endpoint was a composite of ≥ 50% sustained eGFR decline, end-stage kidney disease, and kidney or cardiovascular death. Secondary endpoints included kidney composite endpoint (same as primary composite endpoint but without cardiovascular death), cardiovascular composite endpoint (hospitalized heart failure or cardiovascular death), and all-cause mortality., Key Results: Median follow-up was 2.4 years. Absolute risks of cardiovascular composite endpoint and all-cause mortality were higher in older patients. Absolute risk of kidney composite endpoint was highest in patients < 50 years (10.7 and 6.2 per 100 patient-years in the placebo and dapagliflozin groups, respectively) and lowest in patients ≥ 80 years (3.0 and 1.2 per 100 patient-years in the placebo and dapagliflozin groups, respectively). There was no evidence of heterogeneity of the effects of dapagliflozin on the primary or secondary endpoints based on age or sex. Neither age nor sex modified the effects of dapagliflozin on total or chronic eGFR slope., Conclusions: Dapagliflozin reduced the risks of mortality, cardiovascular events, and CKD progression in older patients, including in septuagenarians and octogenarians who comprised 25% of participants. Ageism and/or therapeutic nihilism should not discourage the use of dapagliflozin in older women and men who are likely to experience considerable benefit., Trial Registry: clinicaltrials.gov NIH TRIAL REGISTRY NUMBER: NCT03036150., (© 2023. The Author(s), under exclusive licence to Society of General Internal Medicine.)

Purpose: This study evaluated the dentin bonding strength and biomineralization effect of a recently developed premixed calcium aluminate-based endodontic sealer (Dia-Root Bio Sealer) in comparison with existing calcium silicate-based sealers., Methods: The root canals of 80 mandibular premolars were filled with Dia-Root Bio Sealer, Endoseal MTA, EndoSequence BC Sealer, and AH Plus Bioceramic Sealer. Medial and apical specimens were then obtained by sectioning. The push-out bond strength was measured using the medial specimens, and the failure mode was recorded. Intratubular biomineralization in the apical specimens was analyzed using scanning electron microscopy and energy-dispersive X-ray spectroscopy (EDS). The data were analyzed using one-way analysis of variance followed by the Tukey test (P < 0.05)., Results: The push-out bond strength of Dia-Root Bio Sealer was significantly higher than that of the other tested materials, and a cohesive failure pattern was observed in all groups. Dia-Root Bio Sealer also exhibited a significantly higher degree of biomineralization than the other groups, and EDS analysis indicated that the biomineralized precipitates were amorphous calcium phosphate., Conclusion: The results of this study indicate that Dia-Root Bio Sealer has the potential to be used as an adequate root canal sealer due to its favorable bonding performance.

Plasmids alter microbial evolution and lifestyles by mobilizing genes that often confer fitness in changing environments across clades. Yet our ecological and evolutionary understanding of naturally occurring plasmids is far from complete. Here we developed a machine-learning model, PlasX, which identified 68,350 non-redundant plasmids across human gut metagenomes and organized them into 1,169 evolutionarily cohesive 'plasmid systems' using our sequence containment-aware network-partitioning algorithm, MobMess. Individual plasmids were often country specific, yet most plasmid systems spanned across geographically distinct human populations. Cargo genes in plasmid systems included well-known determinants of fitness, such as antibiotic resistance, but also many others including enzymes involved in the biosynthesis of essential nutrients and modification of transfer RNAs, revealing a wide repertoire of likely fitness determinants in complex environments. Our study introduces computational tools to recognize and organize plasmids, and uncovers the ecological and evolutionary patterns of diverse plasmids in naturally occurring habitats through plasmid systems., (© 2024. The Author(s).)

Plasmids are extrachromosomal genetic elements that often encode fitness-enhancing features. However, many bacteria carry "cryptic" plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes and is 14 times as numerous as crAssphage, currently established as the most abundant extrachromosomal genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales, and although it does not appear to impact bacterial host fitness in vivo, it can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an alternative approach to track human colonic inflammatory states., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

This study investigated the degree of phase transformation, surface roughness, and bond strength of zirconia immersed for various times in a 40% hydrofluoric acid (HF) solution. Non-etched sintered zirconia specimens were used as the control, while experimental groups were etched with a 40% HF solution for 5, 10, 20, 40, 80, 160 and 320 min. In each of the control and experimental groups, five specimens for X-ray diffraction analysis, four for surface morphology and surface roughness analysis, and ten for bonding strength measurement were used. As a result, the surface roughness of zirconia increased as the application time increased during the 40% HF etching, but the bond strength between zirconia and resin cement did not increase proportionally. The phase transformation from tetragonal to monoclinic also gradually increased with application time.