Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology最新文献

Antibiotic use in aquaculture prevents disease and promotes growth but can disrupt the gut microbiome and drive resistance. The study profiled the gut microbiome of antibiotic-treated Mystus cavasius using both culture-based and shotgun metagenomic approach. Culture-dependent analysis revealed a significant 2–threefold reduction in total viable bacterial count in treated fish. Phylogenetic analysis of 12 cultured isolates revealed treatment-driven enrichment of Bacillus, Enterobacter and Aeromonas. Antibiotic susceptibility testing further revealed increased resistance profiles among isolates from treated fish. Metagenomic profiling identified over 1400 bacterial species and revealed clear taxonomic shifts. Control groups were enriched with beneficial genera such as Lactiplantibacillus and Arthrospira, while treated fish were dominated by opportunistic or resistant taxa including Plesiomonas, Staphylococcus, and Acinetobacter. These shifts were further reflected at the phylum level, with a decline in Proteobacteria and Bacteroidetes, accompanied by an increase in Firmicutes and the enrichment of antibiotic-tolerant lineages. Treated samples exhibited more uniform alpha diversity indices, suggesting a restructuring of the microbial community hierarchy following oxytetracycline exposure, whereas beta diversity analysis showed a moderate separation between control and treated groups. These findings provide critical insights into the ecological and health risks of antibiotic use in aquaculture and underscore the importance of developing sustainable alternatives for disease management in fish farming.

Chronic alcohol consumption alters the composition of the gut microbiota, leading to dysbiosis, increased intestinal permeability, and systemic inflammation, which collectively contribute significantly to the pathogenesis of alcohol-related disorders, encompassing hepatic disease, metabolic abnormalities, immune dysfunction, and neuropsychiatric conditions. The complex interactions of alcohol with the gut ecosystem illuminate the fundamental mechanisms that result in the disruption of the gut-liver axis, the imbalance of microbial metabolites, and the emergence of leaky gut syndrome. The bidirectional gut-brain axis is similarly impaired, intensifying concerns related to addiction and cognitive deficits. Therapeutic strategies, encompassing probiotics, prebiotics, synbiotics, postbiotics, dietary alterations, and fecal microbiota transplantation, offer promising modalities for reinstating microbial balance and alleviating alcohol-induced damage. Cutting-edge treatments such as paraprobiotics and bacteriophage therapy further highlight the potential of microbiome modulation as a viable therapeutic strategy. This review underscores the urgent need for precision-targeted, microbiota-based interventions and calls for expanded clinical research to translate these insights into effective treatments for alcohol-associated disorders.

Graphical Abstract

This paper focuses on the environmental distribution (geographical and temporal) of indigenous yeast between four Mediterranean agroecosystems (barley, faba bean, olive, and vine) and assesses their efficacy as biofertilisers. The analysis indicates high seasonal variations and spatial heterogeneity of yeast communities and density extended between 3 × 10² and 4.5 × 10⁴ CFU/g of soil that depend on five determining factors, which control this distribution, namely, crop type, phenological cycles, rhizospheric effects, vertical stratification, and seasonal variation. These populations are also greatly influenced by pedological characteristics (pH, conductivity and organic matter). Molecular identification of 13 isolates based on their plant growth-promoting (PGP) character displays an extraordinary taxonomic variety, including Candida parapsilosis, Rhodotorula mucilaginosa, Candida membranifaciens, and Schwanniomyces occidentalis. A single isolate (EFOb3) was clustered into the Blastobotrys proliferans complex, although with some quantifiable genetic variation, which suggests the possibility of a divergent lineage that may require further taxonomic research. Inoculation experiments with faba bean and barley show considerable results of promoting growth. The best performance is demonstrated by Rhodotorula mucilaginosa P2Olc1 and led to an enhancement of root biomass by 59.7% in barley and 37.5% in faba bean, with notable impacts on root length (+ 58.7% barley), fresh weight (+ 27.4%), and chlorophyll content (+ 24.4%). It is also remarkable that the C. membranifaciens PFOs2 sample shows exceptional performance, where the growth of barley shoots increases to 36.35%. The statistical superiority of R. mucilaginosa P2Olc1 is confirmed with the inference through principal component analysis (PCA) validating phosphorus solubilisation capacity (SI = 74.97%) and the production of ammonia as well as C. membranifaciens PFOs2, which shows excellent IAA production (31.04 µg/mL). This ecology-biotechnology combination offers a bridge toward sustainable agriculture by decreasing the reliance on chemicals without compromising on agricultural productivity by exploiting and biostimulating native and indigenous microbial resources.

In this study, we aimed to discover and characterize novel Antarctic actinobacteria with potential probiotic benefits for aquaculture, emphasizing their taxonomy, antimicrobial properties, and adaptability to aquaculture environments. Strains H14-L1^T and H35-MC1^T, were isolated from rock samples collected in Horseshoe Island, Antarctica. The strains showed antimicrobial activity against several common fish pathogens, i.e. Aeromonas hydrophila ATCC 7966 ^T, A. hydrophila Ah-2, A. sobria A-sor2, A. sobria ATCC 43979 ^T, Vibrio anguillarum NCIMB6^T and V. anguillarum Va-2, and compatibility with the aquaculture conditions. A combination of phenotypic, chemotaxonomic, and whole-genome analyses was conducted to classify the strains and assess their potential as probiotics. The pairwise comparison of 16S rRNA genes of both strains revealed that the strains were members of the genus Arthrobacter, with the highest pairwise identity values calculated as 99.6% for strain H14-L1^T and ‘A. terrae’ Z1-20 ^T, 99.1% for strain H35-MC1^T and A. polaris C1-1 ^T. However, the overall genome-relatedness indices confirmed that both strains were novel species within the genus Arthrobacter. The chemotaxonomic characterization for polar lipids showed that both strains contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified glycolipid. In addition, the strains contained galactose, glucose, ribose, and trace amounts of rhamnose in their whole-cell sugar hydrolysates. The comprehensive annotation of the genomes for secondary metabolite-coding gene clusters revealed that both strains have genes for terpenes, polyketides and putatively bioactive peptides. The strains exhibited bile tolerance, a moderate level of hydrophobicity and no haemolysis in terms of compatibility with aquaculture conditions. In conclusion, both strains—proposed as Arthrobacter endolithicus sp. nov. and Arthrobacter antibioticus sp. nov.–demonstrated promising probiotic traits and antimicrobial activity, underscoring their potential as novel biocontrol agents in aquaculture. Future in vivo validation and safety assessments are required to confirm their efficacy and facilitate their application in sustainable fish farming.

The Thar Desert, one of the most extreme arid ecosystems, harbours a diverse and resilient microbial community adapted to high temperatures, low moisture, and osmotic stress. In this study, soil samples collected from sand dunes in Churu, Rajasthan, were explored for the isolation of biosurfactant-producing bacteria. A total of ten morphologically distinct bacterial isolates were obtained and screened for biosurfactant activity using drop collapse (DC), emulsification index percentage (EA₂₄) %, surface tension (ST), and interfacial tension (IFT) assays. Among them, three isolates S4, S6, and S9 displayed significant biosurfactant activity. Isolate S9 recorded the highest activity with an EA₂₄% of 57.16 ± 2.63%, ST of 24.61 ± 1.2 mNm⁻¹, and IFT of 4.42 ± 1.26 mNm⁻¹, followed by S6 with an EA₂₄% of 54.13 ± 3.7%, ST of 26.64 ± 2.09 mNm⁻¹, and IFT of 5.81 ± 1.71 mNm⁻¹. Isolate S4 showed an EA₂₄% of 51.83 ± 1.8%, ST of 27.87 ± 1.5 mNm⁻¹, and IFT of 7.39 ± 1.31 mNm⁻¹. The molecular identification through 16S rRNA gene sequencing confirmed that S4 corresponds to Cytobacillus kochii, S6 to Acinetobacter soli, and S9 to Bacillus cereus. These strains demonstrated considerable potential for biotechnological applications, including bioremediation of hydrophobic pollutants and sustainable agriculture. The findings highlight the Thar Desert as an underexplored reservoir of extremophilic, surface-active compound-producing bacteria with noteworthy ecological and industrial relevance.

The oral microbiome, which is known as the diverse and abundant microbial community within the human oral cavity, is an integral part of the human body. The investigation of its composition and functions in both wellness and illness has received notable attention from researchers in recent times. The presence of oral bacteria directly impacts the disease condition of dental caries and periodontal diseases. The oral microbiota interacts dynamically with the host to influence immune regulation and metabolic processes. Advances in sequencing technologies, including whole-metagenome shotgun sequencing, the examination of 16S ribosomal RNA, and meta-transcriptomes, we now possess the capability to comprehensively explore the diversity and functionalities of oral microorganisms, encompassing those that are not amenable to cultivation. As research advances, there is a growing body of evidence suggesting the notable contribution of the oral microbiome to various health conditions, extending beyond ailments solely associated with the oral cavity. This review advances current understanding by presenting a systemic, integrative perspective on the oral microbiome’s role in chronic diseases, offering novel hypotheses and therapeutic directions beyond those explored in prior literature.

Graphical abstract

Oral microbiota and various diseases

Gastroenteritis is a prevalent digestive disorder that contributes to significant morbidity worldwide, often caused by pathogenic bacteria. Probiotics are increasingly recognized for their therapeutic potential in treating gastrointestinal diseases due to their beneficial effects on gut health. This study aimed to explore the antimicrobial, antioxidant, anti-diabetic, and anti-inflammatory properties of Enterococcus faecium metabolites, isolated from a milk sample, against Salmonella enterica. The bacterial strains were isolated using the streak plate method and molecularly characterized, with Enterococcus faecium showing 93.79% sequence similarity and Salmonella enterica showing 96.97% similarity in 16S rRNA sequencing. Metabolites of Enterococcus faecium were extracted using solvents such as ethanol, methanol, n-butanol, and ethyl acetate, resulting in 14 bioactive compounds, including lactic acid, acetic acid, and indole. Antimicrobial activity was evaluated via the disc diffusion method, revealing a dose-dependent increase in the zone of inhibition, reaching 20 mm at 100 µg/mL against Salmonella enterica. Antioxidant activity, assessed using the DPPH assay, exhibited a maximum scavenging rate of 99.8% at 550 µg/mL, while anti-diabetic activity showed 84.66% inhibition of alpha-amylase at 500 µg/mL. The anti-inflammatory activity demonstrated 99% inhibition of protein denaturation at the same concentration. No hemolytic activity was observed at lower concentrations, with the maximum hemolysis of 90% occurring at 250 µg/mL. In conclusion, Enterococcus faecium metabolites exhibited significant in vitro antimicrobial, antioxidant, anti-diabetic, and anti-inflammatory activities, indicating their promise as candidates for further investigation in the context of Salmonella enterica-induced gastroenteritis and related metabolic disorders. Future studies should focus on further clinical applications of these metabolites.

Sodium dodecyl sulfate (SDS), an anionic detergent found in cleaning products and cosmetics, is one of the chemical pollutants in waterways. SDS-utilizing bacteria were isolated from soil and water samples using 0.05% SDS basal medium. Three bacterial isolates were selected for 16S rRNA sequencing based on their ability to solubilize phosphate, potassium, and zinc, and they were identified as Pseudomonas putida MSK86 OR192890, Klebsiella pneumoniae NET12 OR345422, and Enterobacter sp. MSK86 OR398804. Enterobacter sp. MSK86 and K. pneumoniae NET12 lowered the SDS concentration in the sample 84.78% and 75.65%, respectively, while P. putida MSK86 reduced it 33.43% on the sixth day of incubation. A phosphate-potassium-zinc co-inoculum was prepared using Enterobacter and Pseudomonas species. Laundry wash water was added with the bacteria, individually and co-inoculum, and the fortified water was used to irrigate the Capsicum annuum L. seedlings. On the 45th day, the plants were harvested, and total glucose, protein, chlorophyll, and proline were checked by comparing control plants. Enterobacter sp. MSK86 increased carbohydrate and proline levels by 37.22 mg/g (± 0.54 SE) and 2.44 mg/g (± 0.1 SE), while K. pneumoniae NET12-treated plants showed an increase in chlorophyll by 1.95 mg/g (± 0.02 SE) and total protein by 1.94 mg/g (± 0.03 SE). The bacteria in this study showed they could lower SDS levels in graywater and improve farming by adding nutrients to the soil and plants, offering a sustainable way to tackle detergent pollution, fertilizer use, and water scarcity.

The Gram-negative bacterium Xanthomonas campestris pv. campestris is the etiological agent of black rot, a widespread and destructive disease affecting cruciferous plants. In this study, a lon mutant was obtained by EZ-Tn5 transposon mutagenesis of the X. campestris pv. campestris. The lon gene encodes an ATP-dependent protease implicated in protein quality control and stress adaptation across various bacterial species. Functional analysis revealed that lon disruption in X. campestris pv. campestris resulted in diminished extracellular protease activity, reduced virulence, and heightened sensitivity to puromycin and elevated temperatures. Complementation with the wild-type lon allele restored most phenotypes, except thermotolerance, which was only partially recovered. Interestingly, lon overexpression in wild-type cells compromised growth under heat stress, indicating that lon dosage is critical for thermal adaptation. Promoter activity assays indicated that lon expression is subject to catabolite repression and is induced by heat shock. Additionally, analysis of upstream regions of lon and multiple experimentally validated heat-inducible genes revealed a conserved motif similar to the σ³²-binding site in Escherichia coli, suggesting a conserved σ³²-mediated regulatory mechanism. This work provides the functional and regulatory characterization of lon in X. campestris pv. campestris, underscoring its integral role in stress resilience and pathogenicity.

Preen gland bacteria are thought to be the key producers of preen oil components such as chemosignalling molecules including volatile organic compounds (VOCs) and antimicrobial compounds including peptides and antimicrobial VOCs. However, data on the preen oil bacteriome and chemical composition are limited to a small subset of bird species, and the presence of antimicrobial peptides is largely unexplored. Here, we performed an exploratory study to characterize, for the first time, the preen oil chemical and proteomic profiles and to explore the possible contribution of the bacteriome to the production of preen oil VOCs and antimicrobial peptides (bacteriocins) in eight passerine species, each represented by a single individual. Preen oil bacteriome, chemical and proteomic profiles varied among birds. The bacterial profiles were dominated by the genera Streptococcus, Lactococcus, Corynebacterium and Cutibacterium. The chemical profiles mainly consisted of alcohols, ketones and carboxylic acids. The biological functions primarily associated with the proteomic profiles were proteolysis and response to oxidative stress. Although we were unable to explore a direct association between the bacteriome and chemical profiles, the preen oil contained bacteriocin- and VOC-producing bacterial genera capable of producing detected microbially-derived VOCs (mVOCs), the relative abundance of which varied between birds. Riparian species showed the highest chemical diversity and high abundances of putative preen oil mVOC-producing bacteria, which could suggest habitat-specific adaptations. This exploratory study may significantly contribute to the formulation of hypotheses on the potential role of host ecological factors in the variation of preen oil bacterial, chemical and proteomic profiles in passerines.