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Microbiology Research

Microbiology Research is an international, scientific, peer-reviewed open access journal published monthly online by MDPI (from Volume 11 Issue 2-2020).

Quartile Ranking JCR - Q3 (Microbiology)

All Articles (830)

Venomous snakes constitute ecologically significant and medically relevant organisms due to the risks associated with their bites, which frequently result in secondary infections. The oral microbiota of these reptiles plays a crucial role in the pathogenesis of such infections; however, its diversity and clinical implications remain insufficiently characterized. This is the first comprehensive review to systematically trace the methodological evolution in snake oral microbiota research, documenting the paradigm shift from traditional culture-dependent techniques to advanced culture-independent approaches, including next-generation sequencing and metagenomics. Our analysis uniquely demonstrates the transformative impact of these technological advances on bacterial diversity identification and antimicrobial resistance gene detection in venomous species. Environmental factors, captivity conditions, and venom composition significantly influence microbial community structure and resistance profiles. These intricate interactions are essential for improving clinical management of snakebite infections, informing empirical antibiotic therapy protocols, and guiding antivenom production strategies. Additionally, the potential of snake oral microbiota as a source of novel bioactive compounds represents an emerging area of bioprospecting research. This review uniquely bridges microbiology, venomics, and clinical medicine, demonstrating the necessity for integrative, multidisciplinary approaches to fully elucidate the ecological and biomedical significance of oral microbial communities in venomous snakes.

3 November 2025

General workflow for bacterial identification using culture-dependent methods. (a) a biological sample is collected and (b) inoculated onto appropriate culture media, followed by (c) incubation under suitable conditions. After incubation, (d) isolated bacterial colonies are obtained and (e) subjected to Gram staining to differentiate between Gram-positive and Gram-negative bacteria. (f) Pure isolates are then identified using automated systems. This scheme is a general outline; specific steps may vary depending on the bacterial species’ nutritional and atmospheric requirements, as well as the laboratory’s identification equipment. Created in https://BioRender.com. Note: Transport and storage conditions are medium-dependent and must ensure bacterial viability. Incubation parameters (temperature, atmosphere, duration) should be optimized according to target bacterial species and their specific growth requirements. Automated identification platforms utilize diverse methodologies including metabolic profiling, biochemical characterization, and mass spectrometry analysis to achieve species-level classification. Quality control measures and appropriate reference strains are essential for result validation and diagnostic accuracy.

Helicobacter pylori is a gastric pathogen that induces chronic gastritis, which may progress to neutrophilic activity, glandular atrophy, intestinal metaplasia, and gastric carcinoma. The aim of this study was to evaluate H. pylori-induced tissue damage. A total of 602 gastric biopsy samples were collected, categorized, and analyzed using hematoxylin and eosin and Giemsa staining, followed by molecular confirmation through PCR targeting the species-specific 16S rRNA gene. H. pylori density and histopathological features were evaluated and graded according to the updated Sydney classification system. H. pylori was detected in 55% (n = 334) of cases, and the antrum (50.83%, p < 0.00001) was the predominant site. A slightly higher prevalence was observed in females, accounting for 56.9% compared to males at 43.1%, which was attributed to sociocultural exposure differences. Individuals aged 11–40 years accounted for 58.3% (n = 195), highlighting early-age acquisition of infection. H. pylori infection was significantly linked to moderate-to-severe inflammation (63.2%, p < 0.00001) and neutrophilic activity (53.3%, p < 0.00001). Intestinal metaplasia and atrophy were infrequent, present in 0.6% (95% CI, 0.02, p = 0.149) and 0.9% (95% CI, 0.05, p = 0.430) of individuals. H. pylori infection causes chronic inflammation and neutrophilic infiltration of the stomach mucosa. Early identification and histopathological examination are essential in assessing H. pylori-related gastric pathology.

2 November 2025

Identification of H. pylori in gastric tissue. (a) H&amp;E staining (upper row) showed pink-colored spiral-shaped rods (upper arrow). (b) Giemsa staining (lower row) showed that the gastric mucosa revealed curved rod-shaped bacteria (lower arrow).

Staphylococcus spp. are potential pathogens classified into more than 50 species, frequently presenting antimicrobial resistance (AMR) to several drugs. The present study aimed to identify the Staphylococcus species and their AMR in staphylococci isolated from healthy companion animals (pets) in southern Brazil. A total of 78 presumptive Staphylococcus sp. isolates (from 48 dogs and 30 cats) were obtained in a period of five years (2018–2022). All isolates were analyzed by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-ToF) and tested with a panel of antimicrobials frequently used in pet treatment in Brazil. The results demonstrated that 68 isolates were identified as Staphylococcus spp., including 26 (38.2%) classified as coagulase-positive staphylococci (CoPS) and 42 (61.8%) as coagulase-negative staphylococci (CoNS). CoPS included S. pseudintermedius (n = 20; 29.4%), S. aureus (n = 3; 4.4%), and S. schleiferi (n = 2; 2.9%), while CoNS were S. equorum (n = 12; 17.6%), S. felis (n = 7; 10.3%), S. sciuri (n = 8; 11.8%), S. simulans (n = 4; 5.9%), S. epidermidis (n = 1; 1.5%), S. haemolyticus (n = 1; 1.5%), S. saprophyticus (n = 1; 1.5%), and S. xylosus (n = 1; 1.5%). The remaining eight isolates were identified as Staphylococcus spp. AMR analyses demonstrated that 17 (25%) isolates presented susceptibility to all tested drugs, and 51 (75%) to one or more antimicrobials. Twenty-four (35.6%) isolates were multidrug resistant (MDR), and 13 (19.1%) were methicillin-resistant staphylococci (MRS). S. pseudintermedius was the CoPS most frequently with AMR, including nine (45%) MDR and four (20%) MRS, while S. equorum was the predominant CoNS with AMR, highlighting nine (75%) MDR and four (33.3%) MRS. The Staphylococcus species diversity identified here highlights the importance of studying the microorganisms circulating in healthy companion animals and their characteristics concerning pathogenicity and AMR.

31 October 2025

Locations and the respective number of collections carried out between 2018 and 2022.

Sapindus mukorrosi (Sm) seeds have been used in Chinese medicine for treating gingival disease, suggesting that Sm may modulate oral bacteria and alleviate gingival inflammation. However, the hydrophobicity of seed oil limits its use in the aqueous oral environment. Therefore, the artificial saliva-infused Sm seed aqueous extract (SMa) was developed and applied to our ex vivo model to test its anti-bacterial effect. Unstimulated whole saliva from seven patients with Stage III/IV, Grade C periodontitis was cultured for 8 h with or without SMa. The bacterial count was measured based on the optical density and bacterial DNA concentration. The salivary microbiome was sequenced via next-generation sequencing over the 16S rRNA gene V3-V4 hypervariable regions. The bacterial DNA concentration in the SMa group was significantly lower than the Without-SMa group after 6 to 8 h of culture. No significant difference in alpha and beta diversity was observed between the two groups. The relative abundance of Porphyromonas was reduced, while that of Veillonella was elevated in the SMa group compared to the Without-SMa group. The findings indicated that the antibacterial effects of SMa are manifested primarily through bacterial growth inhibition, with the minor modulation of specific taxa.

30 October 2025

(a) OD and (b) DNA concentration of salivary microbiome culture of Without-SMa and SMa groups: represented with median and interquartile range. (ns: not statistically significant, * p &lt; 0.05 based on Wilcoxon signed rank test.).

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Microbiol. Res. - ISSN 2036-7481Creative Common CC BY license