BackgroundExisting evidence supports observational associations between the gut microbiome composition and susceptibility to extraintestinal cancers; however, the causal relationship between gut microbiome composition and the risk of developing head and neck cancer (HNC) remains uncertain. Therefore, we conducted a two-sample Mendelian randomization (MR) analysis using publicly available genome-wide association study (GWAS) data to investigate the potential causal link between gut microbiome composition and HNC.Methods and analysisRelevant investigations were conducted to examine the casualties of exposures and outcomes, using inverse variance weighted (IVW), weighted median (WM) and the MR-Egger method. Sensitivity analyses, including the MR-Egger intercept test, Cochran’s Q test, and leave-one-out analysis, were used to assess pleiotropy and heterogeneity. In addition, the Steiger directionality test was applied to exclude studies with potential directional biases.ResultsOur study identified 16 causal relationships between the genetically predicted abundances of gut microbiota and the risk of developing HNC. After sensitivity analysis on these identified relationships, 10 [class (Actinobacteria, Betaproteobacteria), order Bacillales, family (Ruminococcaceae), genus (Eubacterium_ventriosum_group, Coprococcus2, Coprococcus3, Desulfovibrio, Howardella, Subdoligranulum, Veillonella, Victivallis)] out of the initially identified 16 causal relationships were ultimately validated as being associated with HNC tumors. Steiger directionality test indicated that the MR estimate of causal direction was accurate (All p < 0.05).ConclusionOur MR analysis revealed that the gut microbiome composition was causally associated with the risk of developing HNC and could serve as a new biomarker for preventive and therapeutic strategies for HNC.

Contractile injection systems (CISs) are derivatives of phage tails and are widely distributed in prokaryotes. CISs load cognate effectors and eject them through contractile actions resembling those of phage tails. Ejected effectors play central roles in CIS functionality by acting on target cells and mediating various biological processes. Here, we report a novel group of CIS effectors related to phage tape measure protein, the transmembrane component of the phage infection machinery. This group is broadly distributed within the class Actinobacteria, one of the bacterial classes in which CIS gene clusters are highly conserved, and is represented by Sle1, a cognate effector of the intracellularly localized Streptomyces lividans phage tail-like nanoparticle (SLP). This effector is associated with Sle2, which contains a CIS effector core domain and interacts with the SLP core component. Sle1 is packaged inside SLP and is translocated to lipid membranes along with SLPs. The functional domain of Sle1 enriches the membrane-associated subproteome in S. lividans and E. coli. This effect modifies the physiological properties of S. lividans, ultimately enhancing its adaptation to microbial competition. In addition, we revealed that Sle1-type effectors conserved among actinobacterial species are structurally and functionally diverse in their functional domains. One of them from Micromonospora eburnea constitutes a novel toxin-antitoxin system, and introducing its functional domain into Sle1 reprograms the phenotypic responsiveness of S. lividans to neighboring bacteria. Our findings illustrate that phage elements can be incorporated into CISs as reconfigurable platforms for bacterial adaptation to various environmental conditions.IMPORTANCEBacterial CISs have attracted interest for their importance in microbial ecology and potential in biotechnological applications. However, understanding of their functional diversity is currently limited because many CIS effectors remain unannotated due to a lack of inferable structural and genetic signatures. Our findings on Sle1 and its relatives illuminate a previously unidentified class of CIS effectors with phage tape measure protein-related modular architecture, association with the CIS effector core domain, and wide distribution within the major class of Actinobacteria, substantially expanding the known repertoire of effector classes. The impact of Sle1 on S. lividans suggests a link between CIS effectors and bacterial adaptation to environmental conditions, highlighting unexplored functional diversity of CIS effectors as tuners of bacterial phenotypes in communities.

This study aimed to investigate the changes in the microbiome on the inner surface of clear aligners following the consumption of Coca-Cola. The pH value and bacterial composition on the inner surface of clear aligners were assessed over five wearing cycles in three groups of subjects: those with a normal diet (Group A), those who drank Coca-Cola while wearing the aligners (Group C), and those who drank Coca-Cola after removing the aligners (Group B). Microbial analysis was performed using 16S rRNA gene sequencing and operational taxonomic unit (OTU) abundance profiling. The pH of the fluid inside the aligners significantly decreased immediately after Coca-Cola consumption (0 hour) in Groups B and C (p < 0.05). Group B exhibited the most pronounced decline in pH and alpha diversity at 12 hours, along with the highest beta diversity among the groups (p < 0.05). In Group A, the relative abundances of the phylum Actinobacteria was highest at 0 hour, Bacteroidetes at 12 hours, and class Actinobacteria, Gammaproteobacteria, and species Haemophilus influenzae peaked at 24 hours; conversely, Neisseria subflava showed the lowest abundance compared to Groups B and C (p < 0.05). Compared to Group C, Group B demonstrated higher levels of phylum Fusobacteria at 4 hours and 12 hours, and lower Actinobacteria abundance at 8 hours (p < 0.05). Consumption of Coca-Cola induces unfavorable changes in the microbiome on the inner surface of clear aligners. Notably, drinking Coca-Cola without wearing the aligners resulted in a lower pH and greater microbial imbalance, especially at 12 hours post-consumption.

Gastric cancer (GC) remains a major global health burden, particularly in East Asia, with complex etiologies involving Helicobacter pylori infection, diet, host genetics, and environmental exposures. GC development follows the Correa sequence (CS), a multistep cascade from gastritis to atrophy, erosion, and carcinoma. Although gut microbiota (GM) dysbiosis and metabolic reprogramming have each been implicated in GC, their integrated dynamics across CS remain incompletely defined. We recruited participants across five groups: normal controls (G1), gastritis (G2), atrophy (G3), erosion (G4), and GC (G5). Fecal and gastric tissue samples were analyzed using 16S rRNA sequencing and untargeted metabolomics under both ion modes. Microbial diversity was assessed by α- and β-diversity indices, linear discriminant analysis effect size (LEfSe), and functional prediction. Metabolic features were profiled by UHPLC-Q Exactive Orbitrap MS, and differential metabolites were identified using t-tests and partial least squares discriminant analysis (PLS-DA). Diagnostic potential was evaluated using receiver operating characteristic (ROC) curves. Microbial α-diversity decreased significantly with progression, particularly in G3, while compositional shifts included depletion of Bacteroides and Faecalibacterium alongside enrichment of Actinobacteria, Peptostreptococcaceae, and Lachnoclostridium. LEfSe identified Bifidobacterium and Oscillospiraceae as potential biomarkers of advanced stages. ROC analyses demonstrated strong discriminatory power, with the class Actinobacteria achieving an area under the ROC curve (AUC) of 0.935 in distinguishing controls from GC. Fecal metabolomics revealed reductions in anti-inflammatory short-chain fatty acids (SCFAs) and increases in pro-inflammatory metabolites emerging at G3, while tissue metabolomics showed broader reprogramming in GC involving amino acid, nucleotide, lipid, and energy metabolism. Notably, erosion (G4) exhibited transitional features, whereas atrophy (G3) marked a distinct metabolic "breakpoint". By integrating GM and metabolomic data, this study delineates stage-specific microbial and metabolic alterations along the CS. Atrophy represents a pivotal inflection point in the transition from homeostasis to carcinogenesis, while erosion serves as a transitional state. Combined microbiota-metabolite signatures hold promise for non-invasive early detection, disease stratification, and mechanistic insights into metabolic dependencies in GC.

BackgroundImmune checkpoint inhibitors (ICIs) have improved survival in advanced non-small cell lung cancer (NSCLC), yet reliable biomarkers beyond programmed death-ligand 1 (PD-L1) expression remain limited. Increasing evidence links the gut microbiome to ICI activity, but the predictive value of the salivary microbiome is poorly defined.MethodsWe prospectively analyzed baseline saliva from 71 stage IV NSCLC patients treated with anti–PD-1/PD-L1 (ICI) monotherapy. After quality control, 70 samples underwent 16 S rRNA gene sequencing of the V1–V3 region. Microbial diversity, differential abundance (LEfSe, Mann-Whitney/Kruskal-Wallis with false discovery rate correction) and survival associations (Kaplan-Meier; Cox proportional-hazards with LASSO-based variable selection and 1000-fold bootstrap validation) were examined. In this cohort, an exploratory genus-level cut-off was derived by receiver operating characteristic (ROC) analysis.Results α-diversity and β-diversity did not differ between responders (progression-free survival (PFS) ≥ 12 months; n = 18) and non-responders (n = 52). Differential‑abundance profiling revealed a graded enrichment of the phylum Actinobacteria across all lower ranks, class Actinobacteria, order Actinomycetales, family Actinomycetaceae and genus Actinomyces,in non‑responders (LEfSe LDA > 3.5; p = 0.001 for each level; FDR ≤ 0.049). ROC analysis suggested an Actinomyces relative abundance of 11% (AUC = 0.768; sensitivity 0.94; specificity 0.44) as a data-driven threshold, classifying patients into low (≤ 11%, n = 46) and high (> 11%, n = 24) groups. High abundance was associated with shorter PFS (median 3 vs. 4 months; HR = 2.16, 95% CI 1.21–3.88, p = 0.009) and overall survival (OS) (median 5 vs. 9 months; HR = 2.61, 95% CI 1.48–4.61, p < 0.001) after multivariable adjustment for ECOG status, treatment line, corticosteroid and opioid use, smoking, histology and metastatic sites. Bootstrap validation supported model stability, with median bootstrap HRs of 2.56 (PFS) and 2.63 (OS), with narrow percentile CIs (PFS 1.57–4.49; OS 1.40–6.34) overlapping the original estimates.Conclusions In this exploratory cohort, salivary microbiome signature characterized by high Actinomyces abundance was independently associated with poorer ICI outcomes in NSCLC. Saliva profiling is non-invasive and, if validated in larger and independent cohorts, may complement tumour PD-L1 and clinical factors to refine patient stratification.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12967-025-07570-4.

BackgroundThe mechanisms underlying obesity-related cancer risk are incompletely understood. We investigated whether the gut microbiome causally mediates this relationship.MethodsWe performed two-sample Mendelian randomisation, with mediation analysis, to assess causal links between genetically predicted body mass index (BMI)/waist-to-hip ratio adjusted for BMI (WHRadjBMI), 211 gut microbial taxa, and eight cancers (384,738 cases) of European ancestry. Significant associations were replicated in the FinnGen cohort.ResultsGenetically predicted BMI was associated with risk of colorectal (CRC; odds ratio per standard deviation (ORSD): 1.12; 95% confidence interval (CI): [1.06–1.17]; P = 4.95 × 10−6), kidney (RCC) (ORSD: 1.48; 95% CI: [1.34–1.63]; P = 1.61 × 10−15), endometrial (ORSD: 1.70; 95% CI: [1.55–1.87]; P = 2.09 × 10−27), lung (ORSD: 1.20; 95% CI: [1.12–1.29]; P = 1.40 × 10−7), and oesophageal cancer (ORSD: 1.25; 95% CI: [1.13–1.39]; P = 3.09 × 10−5). Seven microbial taxa were associated with CRC risk. Phylum and class Actinobacteria showed the strongest effects (ORSD: 1.48; 95% CI: [1.29–1.70]; P = 1.78 × 10−8) and (ORSD: 1.36; 95% CI: [1.22–1.51]; P = 2.57 × 10−8), respectively, and replicated in FinnGen, mediating 29% (95% CI: [8-50]) and 21% (95% CI: [4–37]) of the BMI to CRC risk—collectively accounting for 50% of the relationship. No consistent microbiome mediation was observed for other cancers.ConclusionsGut Actinobacteria may contribute to obesity-driven CRC risk, supporting the rationale of microbiome-targeted interventions to reduce CRC risk.

A novel compound denoted MBL-AB01 was isolated from a marine Actinoalloteichus, which belongs to a rare and underexplored class of Actinobacteria. This work demonstrates that the novel compound MBL-AB01 shows very high activity in vitro against six methicillin-resistant Staphylococcus aureus strains, and high activity against a panel of three other Gram-positive strains, including a vancomycin-resistant Enterococcus faecium. Structure elucidation of the compound revealed that MBL-AB01 is a polycyclic xanthone antibiotic closely related to the bioactive compounds: xantholipin and lysolipin. This class of antibiotics has caught interest due to its unique chemical structure and diverse biological activity. The gene cluster encoding MBL-AB01 production was identified, and the individual genes within the cluster were annotated along with proposed functional roles. The compound was produced by bioreactor fermentations, and significantly higher yields of MBL-AB01 were obtained after classical mutagenesis and fermentation process improvements.IMPORTANCEMethicillin-resistant Staphylococcus aureus (MRSA) infections have become a great challenge in hospitals over the last decades, and MRSA is currently one of the six pathogens on the World Health Organization priority list. Here, we demonstrate that the novel antibiotic MBL-AB01 has excellent antibacterial properties against six S. aureus strains, including MRSA. MBL-AB01 belongs to the poorly explored class of polycyclic xanthones, thereby fulfilling innovation criteria for the development of new antibiotics. The compound can be produced in sufficient amounts for early formulation development and pre-clinical trials.

BackgroundSeveral recent studies have confirmed a causal relationship between gut microbiota and Alzheimer's disease (AD), but the potential mediators remain unclear.ObjectiveThis study aimed first to investigate the causal relationship between gut microbiota and AD, and second to explore potential mediators involved in this relationship.MethodsWe used a two-step Mendelian randomization study. Firstly, we mainly used inverse-variance weighted (IVW), weighted median, weighted mode, MR-Egger, and simple mode methods to assess the causal relationship between gut microbiota and AD. Secondly, we conducted mediation analysis to evaluate the roles of inflammatory factors, immune cells, and metabolites in this causal pathway. In addition, we performed sensitivity analysis, Steiger test, and linkage disequilibrium score regression (LDSC).ResultsOur results showed that ten types of gut microbiota were causally associated with AD, of which seven were associated with an increased risk of AD and three with a reduced risk. In addition, the mediation analysis showed that CD45 on Mo MDSC mediated 21.89% of the effect of class Actinobacteria on AD, while the cortisol to taurocholate ratio mediated 18.35% of the effect of genus Lactococcus on AD. Beta-hydroxyisovalerate and glycodeoxycholate levels respectively mediated 10.56% and 16.22% of the effects of class Betaproteobacteria on AD.ConclusionsOur research not only supports modulating gut microbiota as a preventive measure for AD but also emphasizes the mediating roles of inflammatory factors, immune cells, and metabolites. These findings enhance our understanding of the gut-brain axis, providing new perspectives and potential targets for AD prevention.

ABSTRACT An indigenous bacterial strain, designated Nocardiopsis dassonvillei B2, was isolated and identified as a producer of glycolipid biosurfactants, specifically di‐rhamnolipids. The present study focuses on purification, characterization, and biological evaluation of the di‐rhamnolipid biosurfactant. A purified di‐rhamnolipid fraction was obtained using silica gel column chromatography, and its molecular structure was characterized using a combination of infrared (IR) spectroscopy, two‐dimensional nuclear magnetic resonance (2D NMR), and electrospray ionization mass spectrometry (ESI‐MS). The data confirmed that the compound was di‐rhamnolipid, containing two rhamnose sugar molecules attached with fatty acid chain and with mass value 649.93. The NRU assay demonstrated a dose‐dependent decline in cancer cell viability, with IC 50 values of 97.16 ± 0.2 µg/mL for MCF‐7, 217.3 ± 0.5 µg/mL for HCT‐116, and 284.7 ± 0.2 µg/mL for HaCaT cells. The underlying mechanism of action is hypothesized to involve the induction of apoptosis. The di‐rhamnolipid exhibited notable antibacterial activity, with a minimum inhibitory concentration (MIC) of 5 µg/mL against both Gram‐positive and Gram‐negative bacteria, as determined by the agar diffusion method. Furthermore, its strong antibiofilm activity was confirmed against biofilm‐forming pathogens, effectively. These findings establish di‐rhamnolipid as a promising candidate for biomedical applications, including cancer therapy, antimicrobial treatment, and biofilm inhibition, underscoring its potential as a multifunctional therapeutic agent. Practical applications : Nocardiopsis dessonvillei var. B2 produces a di‐rhamnolipid biosurfactant with excellent surfactant and biological activities, similar to other biosurfactant producing strains like Pseudomona s species. Compared to other bacteria, this strain belongs to the class of actinobacteria and is non‐pathogenic to humans, making it very safe for biosurfactant production. The biosurfactant was produced using olive oil as carbon source, as the strain efficiently utilized the oil and generate biosurfactant, which can be useful for the bioremediation of oil contaminated soils, water bodies and other industrial wastes. Further the produced biosurfactant shows potential anticancer, antibiofilm, and antibacterial activities.

Intercropping systems optimize soil ecological functions, modulate microbial diversity, and enhance crop productivity. Arbuscular mycorrhizal fungi (AMF) are key soil symbionts that facilitate nutrient acquisition and enhance stress resilience in host plants. Notably, the AMF spore-associated bacterial communities that play a key role in maintaining AMF spore viability and supporting AMF function remain understudied in intercropping systems. This knowledge gap limits our ability to optimize intercropping's ecological benefits (e.g., enhanced soil fertility, reduced reliance on chemical fertilizers) by leveraging plant-AMF-bacteria synergies, which are critical for sustainable agriculture. This study compared the effects of tomato (Solanum lycopersicum L.) monocropping vs. tomato/potato-onion (Allium cepa L. var. aggregatum G. Don) intercropping on the composition and diversity of AMF spore-associated bacterial communities in the tomato rhizosphere under controlled greenhouse conditions, using Illumina MiSeq sequencing of the 16S rRNA gene V3–V4 region. The results demonstrated that compared with tomato monocropping, tomato/potato-onion intercropping significantly increased the alpha diversity (Shannon and Chao1 indices) of AMF spore-associated bacterial communities in the tomato rhizosphere (Student's t-test, P < 0.05) and markedly altered their taxonomic composition. Taxa significantly enriched under the intercropping system included the phyla Actinobacteriota and Cyanobacteria, the classes Alphaproteobacteria and Actinobacteria (a class of phylum Actinobacteriota), and the genera Janthinobacterium, Rhodococcus, Paenarthrobacter, and Streptomyces. Differential analysis identified 156 significantly shifted OTUs, with 137 enriched (predominantly Proteobacteria/Actinobacteria) and 19 depleted (mostly Bacteroidetes/Proteobacteria) in intercropping. These findings demonstrate that tomato/potato-onion intercropping reshapes AMF spore-associated microbiomes, selectively enriching microbial taxa with putative functions in nutrient cycling and plant growth promotion.

Nocardiosis is a rare but serious infection caused by Nocardia species (class Actinobacteria, order Corynebacteriales). Nocardia is commonly found in soil, dust and plant material, and the infection primarily affects immunocompromised individuals, most often presenting as Pulmonary Nocardiosis (PN) via inhalation. It requires a prolonged course of antimicrobials and is a significant cause of mortality in such patients. PN is often misdiagnosed as Tuberculosis (TB) due to overlapping features, delaying diagnosis and treatment. This case describes a 44-year-old male, a known case of autoimmune hepatitis on corticosteroid therapy, who presented with clinical and radiological features suggestive of pulmonary TB. Modified Kinyoun staining of pleural fluid showed acid-fast, branched, filamentous bacilli and culture grew yellow, chalky colonies identified as Nocardia farcinica. The organism was also isolated on automated and conventional mycobacterial culture media. The patient was successfully treated with cotrimoxazole (double strength). This emphasises the need to include Modified Ziehl-Neelsen (ZN) stain as a rapid screening test to rule out PN and avoid treatment with Antitubercular Therapy (ATT).

The human microbiome includes trillions of bacteria, many of them play essential roles in their owner's physiology. Аim - to systematize data on the effective use of bifidobacteria for various conditions in pediatric patients. The article discusses the mechanisms of formation of the natural intestinal microbiome from birth, which consists mainly of strains of bacteria that produce lactic acid and short-chain fatty acids. Mechanisms of the influence of microbiota on biological processes in the body are presented for attention. The article reviews modern probiotics - drugs that, according to the definition of the World Food Organization and the World Health Organization, contain live beneficial microorganisms that occur naturally in the intestines, remain viable throughout the gastrointestinal tract, and effectively maintain the balance of the intestinal microbiome when administered in sufficient quantities. The basis of probiotics is made up of homofermentative Lactobacteria, which produce only lactic acid, and heterofermentative Bifidobacteria, which belong to the class Actinobacteria (gram-positive bacteria), order Bifidobacteriales and family Bifidobacteriaceae, and which produce both lactic and acetic acid. Given their large numbers in the intestine, especially in young children, their symbiotic relationship with humans, and their contribution to the breakdown of breast milk oligosaccharides, the article reviews the pharmacological aspects of the use of bifidobacteria, which are considered ideal probiotics for infants. Conclusions. A unique complex with two strains of Bifidobacterium breve and innovative protection technology is the optimal choice for maintaining intestinal health in infants, preventing colic, improving digestion in the first months of life and during the introduction of complementary foods, as well as for restoring intestinal function in various pathological conditions. The author declare no conflict of interest.

Ultrasound-assisted extraction was optimized for efficient recovery of plant-based polysaccharides from Ceratonia siliqua pulp. The extracted polysaccharide underwent purification via deproteinization, dialysis, and DEAE-52 ion exchange chromatography, yielding UPS-3, a monodispersed polymer (Mw 1.3 × 103 kDa) composed of mannose, glucuronic acid, glucose, xylose, arabinose, and galactose. UPS-3 exhibited potent antioxidant properties, confirmed by DPPH, ABTS, FRAP, RP, and TAC assays, along with significant α-amylase (98.2 %) and α-glucosidase (95.1 %) inhibition at 2000 μg/mL, highlighting its anti-diabetic potential. Additionally, UPS-3 displayed in vitro anticancer activity against Caco-2 cells and exhibited antibacterial effects against common pathogens. Its prebiotic properties were evidenced by the selective promotion of beneficial gut microbial taxa belonging to the classes Clostridia, Actinobacteria, and Bacteroidia, while inhibiting the potentially pathogenic organisms such as Escherichia and Klebsiella. Fecal fermentation analysis revealed increased production of short-chain fatty acids (SCFAs), including acetate, propionate, and butyrate, emphasizing its role in gut health. Rheological analysis showed its potential as a functional food ingredient with excellent water and oil-holding capacities. These findings suggest that UPS-3 could serve as a natural therapeutic agent for managing metabolic disorders and promoting gut health.

Microbial communities in combination with fatty acid and isotopic markers were studied seasonally to assess the effects of acid mine drainage (AMD) and nutrient loads in the Spree river. Negative values of δ15N, the bacterial and detrital markers 18: 1(n-7) and 18:1(n-9), pH values ∼3 and bacteria of the genera Ferrovum, Thiomonas, Acidocella, Acidiphilum, Syderoxydans and Galionella were characteristic of the AMD extreme. Potential iron-oxidizers may produce ferric ions and their precipitates may influence biogeochemical processes, while potential sulfur-oxidizers may contribute to elevated sulphate concentrations and challenge drinking water production in the Spree catchment. In this river, eutrophication was linked with polyunsaturated fatty acids (PUFA) enrichment and not with PUFA depletion as occurs in other freshwater systems. Elevated concentrations and proportions of PUFA as well as higher relative sequence abundance of cyanobacteria were characteristic of the highly eutrophic station, particularly during the phytoplankton bloom. The 18:5(n-3) from flagellates or dinoflagellates may indicate lipid anabolism and trophic upgrading processes. The dominance of the classes Bacteroidia, Gammaproteobacteria and Actinobacteria suggested eutrophic and changing hydrological conditions in the river. The microbial communities were better markers of seasonality than the biogeochemical markers and their combination offers an excellent resolution for the study of the ecology and biogeochemistry of water courses. The expected decreased runoff under climate-driven scenarios may worsen the AMD pollution and eutrophication problems and signify a considerable challenge for water management.

Specific antiretroviral therapy (ART) regimens are associated with weight gain in people living with HIV (PLWH). Gut microbiota is involved in weight gain in humans and animals. Human gut microbiota can be classified into enterotypes with distinct microbial and functional profiles. In a cohort of 118 PLWH, we analyzed the gut microbiome in relation to weight gain and ART regimen using 16S rRNA gene sequencing, taking enterotype classification into account. The enterotype was strongly associated with sexual orientation. Of the 67 individuals forming a Prevotella-dominated enterotype cluster in principal coordinates analysis, 93% were men who had sex with men (MSM), while 31% of individuals in the Bacteroides-dominated enterotype cluster were MSM and 69% were non-MSM. Forty-nine genera differed significantly between the MSM and non-MSM individuals. When stratified by dominant genus, only six taxa were associated with weight gain. Of these, five were restricted to Bacteroides-dominated individuals. Among them, the class Actinobacteria and genus Bifidobacterium differed between individuals gaining more than 5% weight and less than 5% weight 1 year after ART switch. Additionally, three taxa were significantly different between 15% of individuals with the highest weight gain (≥6.3%) and the highest weight loss (≤3.19%) 1 year after ART switch, including the phyla Firmicutes, Verrucomicrobia, and Synergistetes. Distinct functional properties in Bacteroides, but not Prevotella-dominated enterotype individuals, linked to weight gain were observed, particularly for glycan and lipid metabolism. Additionally, ART regimen-associated differences were observed for the phylum Actinobacteria, although this was limited to Prevotella-dominated enterotype individuals. Differences in the composition and functional characteristics of the gut microbiome associated with weight gain and ART regimens were enterotype-specific and relatively small compared with differences linked to sexual orientation. Due to the substantial differences in gut microbiome structure among many MSM, categorization into enterotypes is useful for identifying differences in microbiome composition associated with variables such as weight gain or ART, which may be limited to a single enterotype. This may further advance the identification of microbes that contribute to weight gain or alter the gut microbiome composition in the context of the enterotype.

The continuous use of antibiotics is associated with many complications in the poultry industry. Probiotics have emerged as a viable alternative over the past few decades to counter the adverse effects of antibiotics. No candidate probiotic microorganisms have been fully evaluated in the poultry industry for their effectiveness as potential probiotics in guinea fowls (GFs) compared to chickens. Recently, a metagenome evaluation of GFs in our laboratory revealed a predominance of Lactobacillus reuteri (L. reuteri) and actinobacteria class of bacteria in their gastrointestinal tract. The aim of this study is to evaluate a well-known lactic acid probiotic bacterium (L. reuteri) and a unique probiotic (S. coelicolor) that has not been assessed in any guinea fowl species. In the current study, L. reuteri and Streptomyces coelicolor (S. coelicolor) were selected as probiotic bacteria, encapsulated, and added into French guinea fowl (FGF) feed individually at a concentration of 108 cfu/g or both microorganisms combined each at 104 cfu/g. In an 8-week study, 216-day-old guinea keets were randomly assigned to four dietary treatments as indicated: (1) L. reuteri (108 cfu/g); (2) S. coelicolor (108 cfu/g); (3) mixture of L. reuteri (104 cfu/g) and S. coelicolor (104 cfu/g); and (4) control treatment (no probiotics included). The L. reuteri, S. coelicolor, and L. reuteri + S. coelicolor were added into the feed using wheat middlings as a carrier at a final concentration of 108 cfu/g. The FGFs that were fed diets containing L. reuteri showed improved feed consumption at 3–8 weeks of age (WOA). The guineas fed L. reuteri and S. coelicolor showed a lower feed conversion ratio (FCR), which was significant at 2 and 8 WOA, and a numerically lower 8-week average FCR when compared with other dietary treatments. Differences in body weight gain among all dietary treatments were not significant. This research suggests that L. reuteri and S. coelicolor may have the potential for use as probiotics in FGFs when used in combination or separately.

Orofacial granulomatosis (OFG) is a rare chronic inflammatory condition. It is under debate, whether it is a condition of its own or merely a subtype of Crohn’s disease (CD). We aimed to search for markers characteristic of patients with pediatric-onset OFG compared to patients with pediatric-onset CD. We recruited young patients with OFG (with or without CD, n = 29), CD (n = 24), and healthy controls (n = 20). All participants provided a fecal sample for microbiota and calprotectin analyses and saliva for DNA analysis of genes associated with OFG and kept a 3-day food diary. Oral disease activity was evaluated using The Oral Disease Activity Score by an otorhinolaryngologist and a dentist. We observed decreased relative abundance in class Clostridia and increased relative abundances of classes Actinobacteria and Bacilli in the feces of patients with OFG when compared to patients with CD and healthy controls. The relative abundances of Bifidobacterium adolescentis increased and Faecalibacterium prausnitzii decreased along with the increase in the Oral Disease Activity Score. We found the NOD2 gene rs8057341 allele A to be enriched in patients with OFG compared to patients with CD. These findings support the theory that OFG is a distinct disease phenotype.

Through implementing a bidirectional Mendelian randomization (MR) study, the causal effects between gut microbiome and polycystic ovary syndrome (PCOS) were analyzed. Summary statistics for PCOS were acquired from the FinnGen consortium R8 release data, which included 27,943 cases and 162,936 controls. The inverse-variance weighting (IVW) method was adopted for analysis. Additionally, the causality involving exposure plus the outcome was evaluated by means of MR-Egger, weighted median, simple mode methods, as well as weighted mode. The IVW estimate showed that the genera Streptococcus plus Enterorhabdus served as protectors of PCOS. By contrast, the phylum Tenericutes, genera Anaerofilum, Coprococcus 2, Lachnospiraceae ND3007 group and Ruminiclostridium 5 were identified as risk elements of PCOS. Based on reverse MR analyses from PCOS on the intestinal microbiome based on the IVW method, the phyla Tenericutes, Actinobacteria, class Actinobacteria, genera Ruminococcaceae UCG004 and Christensenellaceae R 7group exhibited a down-regulation effect after PCOS onset. The genera Bacteroides, Barnesiella, Erysipelotrichaceae UCG003, Ruminococcus gnavus group, and Veillonella were up-regulated. No horizontal pleiotropy or significant IV heterogeneity was observed. We conclude that there is a causality relationship between gut microbiome and PCOS, where some bacterial taxa can be used as biomarkers to promote targeted diagnosis and therapy for PCOS.

Bacterial communities play a crucial role in maintaining the stability of river ecosystems and driving biogeochemical cycling, exhibiting high sensitivity to environmental change. However, understanding the spatial scale effects and assembly mechanisms of riverine bacterial communities under distinct anthropogenic disturbances remains a challenge. Here, we investigated bacterial communities across three distinct watersheds [i.e., intensive urban (UW), intensive agricultural (AW), and natural (NW)] in both dry and wet seasons. We explored biogeographic patterns of bacterial communities and the influence of landscape patterns at multi-spatial scales and water chemistry on bacterial communities. Results showed that α diversity was significantly lower in UW and AW compared to NW, particularly in the dry season. A gradient of β diversity with NW > UW > AW was observed across both seasons (p < 0.05). Pseudomonadota, Bacteroidota, and Actinobacteriota were the most abundant phyla across all watersheds, with specific taxa enriched in each watershed (i.e., the class Actinobacteria was significant enrichment in UW and AW, and Clostridia in NW). The influence of landscape patterns on bacterial communities was significantly lower in human-disturbed watersheds, particularly in UW, where this influence also varied slightly from near riparian buffers to sub-watershed. Homogeneous selection and drift jointly dominated the bacterial community assembly across all watersheds, with homogeneous selection exhibiting a greater influence in UW and AW. Landscape patterns explained less variance in bacterial communities in UW and AW than in NW, and more variance was explained by water chemistry (particularly in UW). These suggest that the stronger influence of species sorting in UW and AW was driven by more allochthonous inputs of water chemistry (greater environmental stress). These findings provide a theoretical foundation for a deeper understanding of riverine bacterial community structure, spatial scale effects, and ecological management under different anthropogenic activities.

Introduction: The genus Rhodococcus, first described by Zopf in 1891, comprises 56 species with validly published names. This bacterium belongs to the phylum Actinobacteria, class Actinobacteria, order Mycobacteriales, and family Nocardiaceae. Notable characteristics of this bacterial genus include: Gram-positive, partially acid-fast positive, catalase-positive, non-spore-forming, and non-motile. The use of molecular methods such as 16S rRNA gene sequencing, along with phenotypic methods, has been suggested for the identification of this bacterium. To date, nine species of the genus Rhodococcus have been reported from clinical specimens. Currently, microbroth dilution is the standard method for assessing the antibiotic susceptibility testing of Rhodococcus species. The pattern of antibiotic resistance in Rhodococcus species varies based on geographical region, and it is recommended that antibiotic susceptibility testing be performed for clinical isolates.