Characterization of Lung Microbiome in Subclinical Pneumonic Thai Pigs Using 16S rRNA Gene Sequencing

Animals, Journal Year: 2025, Volume and Issue: 15(3), P. 410 - 410

Published: Feb. 2, 2025

Bacterial respiratory disease is one of the major concerns in modern pig industry. To address limitations culture-based methods, 16S rRNA sequencing was employed to characterize lung microbiome gain a better understanding microbial physiology and their population genetics. A batch 510 slaughtered pigs from farm located Lampang province, Thailand, selected. Individual weight recorded. total 24 lungs (10 normal 14 pneumonic lungs) were sampled for gross lesion examination communities investigated. Poor growth performance uniformity denoted this batch. Several pathogenic bacteria detected both lungs. Microbial diversity decreased group. PCoA NMDS analysis showed clear separation between groups. Stenotrophomonas spp. (42.12%) dominant genus identified lungs, while Mycoplasma hyopneumoniae (71.97%) most abundant correlating with commonly observed consolidation lesions. The slaughterhouse serves as key checkpoint gathering comprehensive information on health, representative lower tract microbiomics. Monitoring lesions should be implemented routinely regional health.

Language: Английский

---

Insights into human respiratory microbiome under dysbiosis and its analysis tool

Frontiers in Microbiomes, Journal Year: 2025, Volume and Issue: 4

Published: April 28, 2025

The human respiratory tract microbiome is a multi-kingdom microbial ecology that inhabits several habitats along the tract. promotes host health by strengthening immune system and avoiding pathogen infection. lung mostly originates in upper balance between immigration removal determines nature of microbiome. Identification characterization communities from airways have been made much easier recent developments amplicon shotgun metagenomic sequencing data analysis techniques. In pulmonary medicine, there growing interest microbiome, which has linked to illness. However, primary causes bacterial co-occurrence seem be interactions with fungi bacteria as well environmental factors. This study focused on identifying techniques current understanding relationship microbiota various diseases.

Language: Английский

---

Benchmarking of shotgun sequencing depth highlights strain-level limitations of metagenomic analysis

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: March 27, 2025

Abstract Shallow metagenomics promises taxonomic and functional insights into samples at an affordable price. To determine the depth of sequencing required for specific analysis, benchmarking is using defined communities. We used complex mixtures DNA from cultured gut bacteria analysed composition, strain-level resolution, profiles nine depths (0.1-10.0 Gb). Reference-based analysis provided accurate taxonomic, 0.5-1.0 Gb. In contrast, de-novo metagenome-assembled genome (MAG) reconstruction deep (>10 Furthermore, it was found that even high-quality MAGs were chimeric, with few (54.5 %) accurately representing original strains. Functionally, 2 Gb reliable pathway level, but sufficient proteome coverage only achieved 10 Library preparation host-DNA identified as confounders in shallow metagenomic analysis. This comprehensive mock communities provides guidance to increasing community scientists interested metagenomics, highlights limitations capturing diversity.

Language: Английский

---

Shining Light on Oral Biofilm Fluorescence In Situ Hybridization (FISH): Probing the Accuracy of In Situ Biogeography Studies

Molecular Oral Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: April 30, 2025

ABSTRACT The oral biofilm has been instrumental in advancing microbial research and enhancing our understanding of health disease. Recent developments next‐generation sequencing have provided detailed insights into the composition microbiome, enabling species‐level analyses interactions. Fluorescence situ hybridization (FISH) especially valuable for studying spatial organization these microbes, revealing intricate arrangements such as “corncob” structures that highlight close bacterial As more genetic sequence data become available, specificity accuracy existing FISH probes used biogeographical studies require reevaluation. This study examines performance commonly species‐specific probes, designed to differentiate microbes within biofilms, when applied vitro an expanded set strains. Our findings reveal several is compromised, with cross‐species being common than previously assumed. Notably, we demonstrate associations particularly involving Streptococcus Corynebacterium , may need be reassessed align latest metagenomic data.

Language: Английский

---

Fluorescence-based spectrometric and imaging methods and machine learning analyses for microbiota analysis

Microchimica Acta, Journal Year: 2025, Volume and Issue: 192(6)

Published: May 5, 2025

Language: Английский

---

Effect of in utero and lactational exposure to antiretroviral therapy on the gut microbial composition and metabolic function in aged rat offspring

Experimental Biology and Medicine, Journal Year: 2025, Volume and Issue: 250

Published: May 21, 2025

Despite the highly effective impact of antiretroviral therapy (ART) in reducing mother-to-child transmission human immunodeficiency virus (HIV), there are concerns long-term impacts ART on health offspring. The implications perinatal exposure to antiviral drugs gut bacterial population and metabolic function offspring is unclear but may influence outcomes given various reported effects microbiome health. This study aims gain insight into potential effect utero lactational microbiota populations short‐chain fatty acids (SCFAs) production aged rat Pregnant rats were administered a combination (abacavir/dolutegravir/lamivudine) at two different dose levels during gestation throughout lactation, fecal abundance SCFA analyzed when they reached 12 months age. Our results showed dose-dependent sex-based differences microbial taxonomic levels. Specifically, we found decline Firmicutes males, an increase Actinobacteria among males females. Furthermore, sex-specific distribution reorganization Lactobacillus , Bifidobacterium Akkermansia was identified. No significant difference concentration prominent SCFAs IgA These findings provide preliminary information indicating need evaluate more comprehensively future studies, their role outcomes.

Language: Английский

---

Gut microbiome is associated with recurrence-free survival in patients with resected Stage IIIB-D or Stage IV melanoma treated with immune checkpoint inhibitors

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 20, 2024

Summary The gut microbiome (GMB) has been associated with outcomes of immune checkpoint blockade therapy in melanoma, but there is limited consensus on the specific taxa involved, particularly across different geographic regions. We analyzed pre-treatment stool samples from 674 melanoma patients participating a phase-III trial adjuvant nivolumab plus ipilimumab versus nivolumab, three continents and five Longitudinal analysis revealed that GMB was largely unchanged following treatment, offering promise for lasting GMB-based interventions. In region-specific cross-region meta-analyses, we identified taxonomic markers recurrence, including Eubacterium, Ruminococcus, Firmicutes , Clostridium . Recurrence prediction by these best achieved regions matching participants compositional similarity between intra-regional discovery external validation sets. AUCs ranged 0.83-0.94 (depending initial region) closely matched composition (e.g., JSD ≤0.11). This evidence indicates recurrence are generalizable regions, individuals similar composition. Highlights Overall during ICB treatment. varies region bacterial analyses. Region-identified if taken into account matching.

Language: Английский

---

The Role of Prevotella Species in Female Genital Tract Infections

Pathogens, Journal Year: 2024, Volume and Issue: 13(5), P. 364 - 364

Published: April 28, 2024

Female genital tract infections (FGTIs) include vaginal (e.g., bacterial vaginosis [BV]), endometritis, pelvic inflammatory disease [PID], and chorioamnionitis [amniotic fluid infection]. They commonly occur in women of reproductive age are strongly associated with multiple adverse health outcomes including increased risk HIV/sexually transmitted infection acquisition transmission, infertility, birth such as preterm birth. These FGTIs characterized by a disruption the cervicovaginal microbiota which largely affects host immunity through loss protective, lactic acid-producing Lactobacillus spp. overgrowth facultative strict anaerobic bacteria. Prevotella species (spp.), Gram-negative rods, implicated pathogenesis FGTIs. Specifically, P. bivia, amnii, timonensis have unique virulence factors this setting, resistance to antibiotics used treatment. Additionally, evidence suggests that presence untreated BV cases can lead upper female ascension into uterus. This narrative review aims explore most common FGTIs, highlight their important role propose future research area.

Language: Английский

---

Gut microbiota, blood metabolites, and left ventricular diastolic dysfunction in US Hispanics/Latinos

Microbiome, Journal Year: 2024, Volume and Issue: 12(1)

Published: May 10, 2024

Abstract Background Left ventricular diastolic dysfunction (LVDD) is an important precursor of heart failure (HF), but little known about its relationship with gut dysbiosis and microbial-related metabolites. By leveraging the multi-omics data from Hispanic Community Health Study/Study Latinos (HCHS/SOL), a study population at high burden LVDD, we aimed to characterize microbiota associated LVDD identify metabolite signatures incident LVDD. Results We included up 1996 Hispanic/Latino adults (mean age: 59.4 years; 67.1% female) comprehensive echocardiography assessments, microbiome, blood metabolome data. was defined through composite criterion involving tissue Doppler assessment left atrial volume index measurements. Among participants, 916 (45.9%) had prevalent 212 out 594 participants without baseline developed over median 4.3 years follow-up. Using multivariable-adjusted analysis compositions microbiomes (ANCOM-II) method, identified 7 512 dominant bacterial species (prevalence > 20%) ( FDR-q < 0.1), inverse associations being found for Intestinimonas_massiliensis , Clostridium_phoceensis Bacteroide_coprocola positive Gardnerella_vaginali Acidaminococcus_fermentans Pseudomonas_aeruginosa Necropsobacter_massiliensis . multivariable adjusted linear regression, 220 669 circulating metabolites detection rate 75% were LVDD-related majority linked Furthermore, 46 these bacteria-associated metabolites, mostly glycerophospholipids, secondary bile acids, amino 21 which (relative risk ranging 0.81 [ p = 0.001, guanidinoacetate] 1.25 9 × 10 −5 1-stearoyl-2-arachidonoyl-GPE (18:0/20:4)]). The inclusion bacterial-related significantly improved prediction compared traditional factor model (the area under receiver operating characteristic curve [AUC] 0.73 vs 0.70, 0.001). Metabolite-based proxy association analyses revealed Intestinimonas_massilliensis Conclusion In this US Hispanics/Latinos, multiple bacteria related suggesting their potential roles in preclinical HF entity.

Language: Английский

---

Fine-scale characterization of the soybean rhizosphere microbiome via synthetic long reads and avidity sequencing

Environmental Microbiome, Journal Year: 2024, Volume and Issue: 19(1)

Published: July 12, 2024

The rhizosphere microbiome displays structural and functional dynamism driven by plant, microbial, environmental factors. While such plasticity is a well-evidenced determinant of host health, individual community-level microbial activity within the remain poorly understood, due in part to insufficient taxonomic resolution achieved through traditional marker gene amplicon sequencing. This limitation necessitates more advanced approaches (e.g., long-read sequencing) derive ecological inferences with practical application. To this end, present study coupled synthetic technology avidity sequencing investigate eukaryotic prokaryotic dynamics soybean (Glycine max) under field conditions.

Language: Английский

---