Current Microbiology最新文献

The present study explores the microbial community associated with the industrially important red seaweed Gracilaria dura to determine the diversity and biotechnological potential through culture and metagenomics approaches. In the first part of the investigation, we isolated and characterized 75 bacterial morphotypes, with varied colony characteristics and metabolic diversity from the wild seaweed. Phylogenetic analysis identified isolates in Proteobacteria, Firmicutes, and Actinobacteria, with Bacillus sp. being prevalent. B. licheniformis and Streptomyces sp. were notable in producing important enzymes like L-asparaginase, and polysaccharide lyases. Antimicrobial activity was significant in 21% of isolates, effective against seaweed pathogens such as Vibrio and Xanthomonas. Rhodococcus pyridinivorans showed strong pyridine degradation, suggesting bioremediation potential. Several isolates exhibited phosphate solubilization and nitrate indicating the roles of bacteria as algal growth promoters and biocontrol agents. Subsequent metagenome analysis of wild and cultured samples provides insights into bacterial communities associated with G. dura, revealing their distribution and functional roles. Proteobacteria (~ 95%) dominated the communities, further bacterial groups involved in algal growth, carpospore liberation, stress resistance, biogeochemical cycles, and biomedical applications were identified. A notable difference in bacteriomes was observed between the samples, with 25% remaining stable. The samples are cultured in the lab to generate seedlings for farming and serve as germplasm storage during the monsoon season. Microbiome surveys are crucial for understanding the association of pathogens and the overall health of the seedlings, supporting successful seaweed farming. Our findings provide valuable insights into G. dura-associated microbial communities and their role in algal growth, which has aquacultural implications.

A facultative anaerobic, Gram-stain-negative, non-motile, rod-shaped bacterial strain AGMB14963^T was isolated from the feces of a dairy cow. A 16S rRNA gene sequence-based phylogenetic analysis revealed that strain AGMB14963^T belongs to the genus Gallibacterium, with Gallibacterium salpingitidis F150^T being the closest species (95.8% 16S rRNA gene sequence similarity). Whole-genome sequence analysis revealed that strain AGMB14963^T had a 37.0% G + C genomic DNA content and a genome size of 2.58 Mb. In addition, the strain contained 53 tRNA and 2 rRNA genes. The average nucleotide identity and digital DNA-DNA hybridization values between strains AGMB14963^T and G. salpingitidis F150^T were 82.3 and 24.9%, respectively. Further, strain AGMB14963^T was positive for oxidase and catalase, but negative for urease. Optimal growth of strain AGMB14963^T occurred at 37 ℃, pH 8, and in 0.5% NaCl-containing medium. The predominant cellular fatty acids (> 10%) in strain AGMB14963^T were C_14:0, C_16:0, and summed feature 3. Strain AGMB14963^T produced lactic acid and isobutyric acid as the major end products of glucose fermentation. Polar lipids consisted of one phospholipid and one phosphoaminolipid. According to the genomic, physiologic, and chemotaxonomic characteristics, strain AGMB14963^T represents a novel species of the genus Gallibacterium, for which the name Gallibacterium faecale sp. nov. is proposed. The type strain is AGMB14963^T (= KCTC 25487 ^T = NBRC 116419 ^T).

A novel phosphate-solubilizing and zinc-solubilizing actinobacterium strain YIM S08009^T was isolated from rhizosphere soil collected from Pinus yunnanensis in Wuliangshan National Nature Reserve, Pu'er City, Yunnan Province, southwest PR China. Cells of strain YIM S08009^T were Gram-stain-positive, non-motile, irregular rods to cocci, and formed yellow and white colonies on nutrient agar. Growth was observed at 10-40 °C (optimum 25-35 °C), pH 6.0-8.5 (optimum 7), and 0-4% (w/v) NaCl (optimum 1%). The cell wall peptidoglycan contained LL-diaminopimelic acid. The whole-cell sugars were mannose, ribose, glucose, and galactose. The predominant menaquinone was MK-8(H₄). Major polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, unknown lipid, and 3 unknown phospholipids. The predominant fatty acids were iso-C_14:0, iso-C_15:0, and iso-C_16:0. The DNA G + C content was 72.6%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM S08009^T belonged to genus Intrasporangium, and was most closely related to Intrasporangium flavum MUSC 78^T, with 99.0% 16S rRNA gene sequence similarity. Strain YIM S08009^T shared 90.1% orthologous average nucleotide identity (OrthoANI) and 39.8% digital DNA-DNA hybridization (dDDH) with I. flavum MUSC 78^T. The genome of strain YIM S08009^T contained phosphate-solubilizing genes (SenX3, RegX3, pstSCAB, ugpBAEC, phoA) and zinc-solubilizing genes (znuABC, zupT), and the strain had also demonstrated in vitro phosphorus and zinc solubilization. Based on the genotypic and phenotypic analyses, strain YIM S08009^T (= CGMCC 1.60168^T = NBRC 116604^T = KCTC 59021^T) represents a novel Intrasporangium species, for which the name Intrasporangium zincisolvens sp. nov. is proposed.

Endophytic fungi are non-pathogenic organisms that colonise healthy plant tissues asymptomatically. Endophytes derived from medicinal plants are sources for identifying natural products and bioactive compounds with potential uses for industry, medicine, agriculture, and related sectors. In the present study, ethyl acetate crude extracts of four endophytic fungal isolates (CALF1, CALF4, and CASF1) from the medicinal plant Plectranthus amboinicus showed potent antimicrobial activity against the test pathogenic bacteria Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Bacillus subtilis using disc diffusion assays. A colorimetric microdilution assay to detect the minimum inhibitory concentration (MIC) revealed that the extracellular extract (ECE) of CASF1 isolate had the lowest MIC values against the test pathogenic bacteria (0.19-6.25 mg/ml) compared to other CALF1 and CALF4. Cytotoxic activity of CASF1-ECE against the drug-resistant KB.CHR.8-5 cancer cell line tested by the MTT assay showed complete cell death at a concentration of 220 μg/mL and the half-maximum inhibitory concentration (IC₅₀) was determined to be 77.9 ± 09 μg/mL. GC-MS analysis showed hexadecanoic acid, 2-hydroxy-1-(hydroxymethyl) ethyl ester, as the dominant compound among the bioactive compounds identified in the EXE of CASF1 isolate, with the highest peak in the GC chromatogram, indicating its role in the antimicrobial and cytotoxic activity of CASF1. Molecular identification of CASF1 using 18S rRNA sequencing and BLAST analysis detected CASF1 as an isolate of Aspergillus versicolor with 100% sequence identity.

Abies pindrow, a vital conifer in the Kashmir Himalayan forests, faces threats from low regeneration rates, deforestation, grazing, and climate change, highlighting the urgency for restoration efforts. In this context, we investigated the diversity of potential culturable seed endophytes in A. pindrow, assessed their plant growth-promoting (PGP) activities, and their impact on seed germination and seedling growth. We cultured 729 microbial isolates that were resolved into 30 bacterial and 18 fungal species across various phyla. All 48 isolates exhibited various PGP activities. Specifically, all the cultured isolates showed IAA activity with concentrations ranging from 2.07 to 8.453 μg/ml, while ammonia production ranged from 0.936 to 3.436 mM/ml. Only 18 isolates, predominantly fungi, tested positive for phosphate solubilisation. Additionally, 20 isolates exhibited the ability to inhibit the growth of Fusarium oxysporum f.sp. pini. We selected four bacterial and six fungal isolates, which showed positive results for all PGP activities, to evaluate their effects on seed germination and seedling growth. Notably, seed germination rates increased by 750.9% under bacterial and consortium treatments and by 550.45% under fungal treatment. The consortium treatment also led to a 96% increase in needle count, while bacterial treatment enhanced stem length by 55.4%. Furthermore, shoot biomass also showed a significant increase with both bacterial and fungal treatments, underscoring the potential of harnessing seed endophytes to boost A. pindrow seedling health and resilience. This study underscores the crucial role of seed endophytic diversity in enhancing seed germination, seedling growth, and forest restoration efforts.

Sporadic epidemics of coxsackievirus A4 (CVA4) have been reported worldwide. However, the lack of the whole genome sequence has restricted the study of the gene characterization and evolution of CVA4. In this study, four whole genome sequences and 17 VP1 sequences of CVA4 identified from Linyi, northern China, in summer 2024 were used for genetic characterization and phylogenetic analysis. Four genotypes (A, B, C, and D) and five subgenotypes (C1-C5) were identified based on VP1 sequences. The Linyi CVA4 strains belong to subgenotype C2, which has also been the main prevalent subgenotype in China in recent years. The Linyi CVA4 strains exhibited high homology with the CVA4 prototype strain in the P1 region while exhibited higher homology with some non-CVA4 EV-A strains identified in China, including five CVA2 strains, three CVA5 strains, three CVA6 strains, one CVA8 strain, one CVA12 strain, and one CVA14 strain in the P2 and P3 regions. Recombination analysis of the whole genome sequences of the Linyi CV4 strains revealed that two Linyi CVA4 strains might be recombinants of one Shanghai CVA4 strain (KJ541163) and one Jiangsu CVA2 strain (OL519580). One Linyi CVA4 strain might be a recombinant of one Shandong CVA2 strain (MK967660) and one Shanghai CVA4 strain (KJ541163).

The fish intestine is a complex ecosystem where microbial communities are dynamic and influenced by various factors. Preservation conditions during field collection can introduce biases affecting the microbiota amplified during sequencing. Therefore, establishing effective, standardized methods for sampling fish intestinal microbiota is crucial. This study used hybrid groupers (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂) to examine the effects of six preservation methods: dry ice (1 day), dry ice (1 day) followed by - 80 °C storage (5 days), liquid nitrogen (1 day), liquid nitrogen (1 day) with subsequent - 80 °C storage (5 days), refrigeration at 4 °C (3 days), and freezing at - 20 °C (3 days), with fresh samples as controls. High-throughput 16S rRNA sequencing assessed microbial diversity, community structure, dominant species, and OTU abundance across treatments. Results indicated that dry ice and liquid nitrogen methods, especially with - 80 °C storage, had minimal impact on microbial diversity and structure. Compared to other preservation methods, refrigeration at 4 °C and freezing at - 20 °C may result in suboptimal reproducibility and altered community structure, particularly affecting rare microbial taxa. This study underscores the need for standardized preservation techniques to ensure accurate fish intestinal microbiota analysis and provides a foundation for future research.

Brucella spp. is the bacterium responsible for brucellosis, a zoonotic infection that affects humans. This disease poses significant health challenges and contributes to poverty, particularly in developing countries. This study aimed to assess the seroprevalence, risk factors, and clinical symptoms of human brucellosis within the general population of Multan and Muzaffargarh, Pakistan. A total of 307 blood samples were collected from patients visiting local hospitals in Multan and Muzaffargarh between August 2015 and January 2016. Demographic information, risk factors, and clinical outcomes were documented. Serum samples were initially screened for anti-Brucella antibodies using the Rose Bengal Plate Test, and positive cases were subsequently confirmed through RT-PCR. The chi-square test assessed the link between Brucella positivity and the identified risk factors. The study recorded an overall seroprevalence of 6.8%, with 8.9% in Multan and 4.3% in Muzaffargarh. Genus-specific Brucella detection through RT-PCR confirmed that 20 out of 21 samples were positive. Significant associations with human brucellosis were found for contact with aborted animals (p = 0.032) and consumption of raw milk (p = 0.031), while factors such as age, gender, occupation, urbanicity, and geographical region did not show a significant impact on seropositivity (p > 0.05). Non-specific clinical symptoms were commonly observed among seropositive patients. The findings highlight the significance of close human interaction with infected animals, especially concerning livestock practices and dairy product consumption. The results also emphasize the importance of focusing efforts on raising awareness in risky occupations and developing control programs by healthcare authorities.

Interactions with mycorrhizal fungi are increasingly recognized as crucial ecological factors influencing orchids' distribution and local abundance. While some orchid species interact with multiple fungal partners, others show selectivity in their mycorrhizal associations. Additionally, orchids that share the same habitat often form relationships with different fungal partners, possibly to reduce competition and ensure stable coexistence. However, the direct impact of variations in mycorrhizal partners on seed germination remains largely unknown. We examined how fungal associates' specific identity and origin affect seed germination in Spiranthes spiralis and Serapias orientalis through in situ symbiotic germination experiments. A total of four fungal isolates, Tulasnellaceae and Ceratobasidiaceae were successfully isolated and cultured from S. spiralis and S. orientalis and two additional orchid species  found in the same habitat: Neotinea tridentata and Orchis provincialis. While all fungal strains facilitated the swelling of seed embryos, only the fungal associate, a member of the Ceratobasidiaceae family isolated from N. tridentata, (NT2) was capable of inducing protocorm formation and subsequent seedling growth of S. spiralis seeds. Another fungal associate belonging to the Tulasnellaceae family and isolated from O. provincialis (OP3) supported seed germination up to the seedling stage of S. orientalis seeds. However, the remaining two fungal strains did not support seed germination. We conclude that fungal associates of co-occurring orchids can promote seed germination and seedling growth in S. spiralis and S. orientalis.

Staphylococcus epidermidis (S. epidermidis) live in different human locations and natural environments. For ribotyping S. epidermidis sub-species, 2507 PCR-amplified reads of 16S rRNA genes of S. epidermidis in a public dataset were used for probabilistic sequence analysis. A sequence probability logo (sequence pLogo) as a reference sequence of 16S rRNA genes of S. epidermidis was constructed. Through implementation of Levenshtein Distance algorithm, two 20-base pairs (bp) motifs, commonly present in 2507 PCR-amplified reads, were identified. The top 38 S. epidermidis isolates, which carried 16S rRNA nucleotide domains that were made of different sequences but have high similarity scores to two 20-bp motifs, were found from 11 human, 8 animal, 9 plant and 10 environmental samples, indicating that these two 20-bp motifs were broadly present in diverse S. epidermidis isolates. Thirty-one PCR-amplified reads of 16S rRNA genes, which were currently not in the dataset, were utilized to verify the feasibility of using two 20-bp motifs for ribotyping S. epidermidis sub-species. S. epidermidis S1, S3, but not S2, isolates on the human scalp carried a 20-bp sequence domain with high similarities to a 20-bp motif in the sequence pLogo. The phylogenetic tree showed that S. epidermidis S1, S2 and S3 were not from a single common ancestor. Two newly identified 20-bp motifs here, thus, provided reference nucleotide residues for ribotyping S. epidermidis.