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Keywords = aerobic and anaerobic cultures

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14 pages, 1209 KiB  
Article
Generation of Nitrous Oxide by Aerobic Denitrifiers Isolated from an Urban Wetland in Bogotá, Colombia
by Maribeb Castro-González and Verónica Molina
Limnol. Rev. 2025, 25(3), 32; https://doi.org/10.3390/limnolrev25030032 - 15 Jul 2025
Viewed by 180
Abstract
In this study, we evaluated the nitrous oxide production potential of denitrifying bacterial strains isolated from sediments of the urban wetland Santa María del Lago under anaerobic and aerobic conditions to determine their potential role in mitigating anthropogenic N2O emissions, which [...] Read more.
In this study, we evaluated the nitrous oxide production potential of denitrifying bacterial strains isolated from sediments of the urban wetland Santa María del Lago under anaerobic and aerobic conditions to determine their potential role in mitigating anthropogenic N2O emissions, which have increased by approximately 40% since 1980, and if these emissions could be related to the absence of the nitrous oxide reductase gene (nosZ). The results demonstrated that denitrifying bacteria belonging to the genus Bacillus were able to generate nitrous oxide in high concentrations under both aerobic (up to 83 nM/h) and anaerobic (up to 3865.5 nM/h) conditions in cultures with optimal concentrations of nitrate and carbon. The amplification of the nosZ gene as marker of denitrifying microorganisms showed that only 50% of strains possess this gene, and its presence did not correlate with nitrous oxide reduction under anoxic conditions. Interestingly, one strain was able to reduce nitrous oxide in the presence of air, which is promising for its potential use in aerobic bioremediation systems that require microorganisms with a high affinity for this greenhouse gas to reduce emissions into the atmosphere. Full article
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16 pages, 4376 KiB  
Article
Enhanced Biogas Production from Glucose and Glycerol by Artificial Consortia of Anaerobic Sludge with Immobilized Yeast
by Nikolay Stepanov, Olga Senko, Aysel Aslanli, Olga Maslova and Elena Efremenko
Fermentation 2025, 11(6), 352; https://doi.org/10.3390/fermentation11060352 - 17 Jun 2025
Viewed by 644
Abstract
Today, there is considerable interest in creating artificial microbial consortia to solve various biotechnological problems. The use of such consortia allows for the improvement of process indicators, namely, increasing the rate of accumulation of target products and enhancing the conversion efficiency of the [...] Read more.
Today, there is considerable interest in creating artificial microbial consortia to solve various biotechnological problems. The use of such consortia allows for the improvement of process indicators, namely, increasing the rate of accumulation of target products and enhancing the conversion efficiency of the original substrates. In this work, the prospects for creating artificial consortia based on anaerobic sludge (AS) with cells of different yeasts were confirmed to increase the efficiency of methanogenesis in glucose- and glycerol-containing media and obtain biogas with an increased methane content. Yeasts of the genera Saccharomyces, Candida, Kluyveromyces, and Pachysolen were used to create the artificial consortia. Their concentration in the biomass of consortium cells was 1.5%. Yeast cells were used in an immobilized form, which was obtained by incorporating cells into a cryogel of polyvinyl alcohol. The possibility of increasing the efficiency of methanogenesis by 1.5 times in relation to the control (AS without the addition of yeast cells) was demonstrated. Using a consortium composed of methanogenic sludge and yeast cells of the genus Pachysolen, known for their ability to convert glycerol into ethanol under aerobic conditions, the possibility of highly efficient anaerobic conversion of glycerol into biogas was shown for the first time. Analysis of the metabolic activity of the consortia not only for the main components of the gas phase (CH4, CO2, and H2) and metabolites in the cell culture medium, but also for the concentration of intracellular adenosine triphosphate (ATP), controlled by the method of bioluminescent ATP-metry, showed a high level of functionality and thus, prospects for using such consortia in methanogenesis processes. The advantages and the prospect of using the developed consortia instead of individual AS for the treatment of methanogenic wastewater were confirmed during static tests conducted with several samples of real and model waste. Full article
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13 pages, 462 KiB  
Article
Clinical Characteristics of Patients with Intra-Abdominal Infection Caused by Stenotrophomonas maltophilia
by Chien-Liang Chen, Chun-Chou Tsai, Wei-Ping Chen, Feng-Yee Chang, Ching-Mei Yu, Hung-Sheng Shang, Leung-Kei Siu, Ya-Sung Yang, Jung-Chung Lin and Ching-Hsun Wang
J. Clin. Med. 2025, 14(11), 3974; https://doi.org/10.3390/jcm14113974 - 4 Jun 2025
Viewed by 598
Abstract
Background: Intra-abdominal infections (IAIs) caused by Stenotrophomonas maltophilia have rarely been reported. This study aimed to describe the clinical characteristics and risk factors for mortality among patients with S. maltophilia IAIs. Methods: A retrospective study was conducted on inpatients with IAIs caused by [...] Read more.
Background: Intra-abdominal infections (IAIs) caused by Stenotrophomonas maltophilia have rarely been reported. This study aimed to describe the clinical characteristics and risk factors for mortality among patients with S. maltophilia IAIs. Methods: A retrospective study was conducted on inpatients with IAIs caused by S. maltophilia at Tri Service General Hospital from 2004 to 2017. Clinical and microbiologic data of the included cases were reviewed via medical charts and microbiology databases. Multivariable logistic regression analyses were performed to identify risk factors for in-hospital death. Results: In total, 110 patients were diagnosed with S. maltophilia IAIs. Malignancy (56.3%) and liver cirrhosis (35.3%) were the most commonly identified underlying diseases. The major causes of S. maltophilia IAIs were biliary tract infection (42.7%), recent abdominal surgery (35.4%), and spontaneous bacterial peritonitis (20.0%). Polymicrobial infections were observed in 84 (76.4%) patients. In addition to S. maltophilia, co-cultured bacteria (n = 140) included Enterobacterales, representing 19.3% (27/140) of the total isolates, and non-fermentative aerobes, comprising 29.3% (41/140). In addition, anaerobic bacteria and fungi accounted for 9.2% (13/140) and 10% (14/140), respectively. The overall mortality rate was 40.9%. Multivariable logistic regression analysis revealed that high Sequential Organ Failure Assessment scores and malignancies were independent risk factors for mortality, while the immediate administration of appropriate antibiotics targeting S. maltophilia was a protective factor (p < 0.05). Conclusions: Patients with an underlying malignancy or liver cirrhosis were at risk for IAIs caused by S. maltophilia. The prompt initiation of effective antibiotics against S. maltophilia is critical for achieving favorable outcomes. Full article
(This article belongs to the Section Infectious Diseases)
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16 pages, 6717 KiB  
Article
Ureolysis-Driven Microbially Induced Carbonate Precipitation by a Facultatively Anaerobic Thermophilic Bacterium Under High-Temperature and Anaerobic Conditions
by Xiulun Shen, Sijia He, Yutaro Takaya, Tomoyoshi Yakata, Kotaro Yoshida and Hajime Kobayashi
Microorganisms 2025, 13(5), 1102; https://doi.org/10.3390/microorganisms13051102 - 10 May 2025
Viewed by 615
Abstract
Microbially induced carbonate precipitation (MICP) is the precipitation of CaCO3 crystals, induced by microbial metabolic activities such as ureolysis. Various applications of MICP have been proposed as innovative biocementation techniques. This study aimed to verify the feasibility of ureolysis-driven MICP applications in [...] Read more.
Microbially induced carbonate precipitation (MICP) is the precipitation of CaCO3 crystals, induced by microbial metabolic activities such as ureolysis. Various applications of MICP have been proposed as innovative biocementation techniques. This study aimed to verify the feasibility of ureolysis-driven MICP applications in deep-subsurface environments (e.g., enhanced oil recovery and geological carbon sequestration). To this end, we screened sludge collected from a high-temperature anaerobic digester for facultatively anaerobic thermophilic bacteria possessing ureolytic activity. Then, we examined the ureolysis-driven MICP using a representative isolate, Bacillus haynesii strain SK1, under aerobic, anoxic, and strict anaerobic conditions at 30 °C, 40 °C, and 50 °C. All cultures showed ureolysis and the formation of insoluble precipitates. Fourier transform infrared spectroscopy analysis revealed precipitates comprising CaCO3 at 30 °C, 40 °C, and 50 °C under aerobic conditions but only at 50 °C under anoxic and strict anaerobic conditions, suggesting efficient MICP at 50 °C. Interestingly, an X-ray diffraction analysis indicated that calcium carbonate crystals that were produced under aerobic conditions were in the form of calcite, while those that were produced under anoxic and strict anaerobic conditions at 50 °C were mostly in the form of vaterite. Thus, we demonstrated ureolysis-driven MICP under high-temperature and O2-depletion conditions, suggesting the potential of MICP applications in deep-subsurface environments. Full article
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11 pages, 1028 KiB  
Article
Potential for Misinterpretation in the Laboratory Diagnosis of Clostridioides difficile Infections
by Alexandra Kalacheva, Metodi Popov, Valeri Velev, Rositsa Stoyanova, Yordanka Mitova-Mineva, Tsvetelina Velikova and Maria Pavlova
Diagnostics 2025, 15(9), 1166; https://doi.org/10.3390/diagnostics15091166 - 3 May 2025
Viewed by 611
Abstract
Background/Objective. Toxin-producing strains of Clostridioides difficile (C. diff) are the most commonly identified cause of healthcare-associated infection in the elderly. Risk factors include advanced age, hospitalization, prior or concomitant systemic antibacterial therapy, chemotherapy, and gastrointestinal surgery. Patients with unspecified and [...] Read more.
Background/Objective. Toxin-producing strains of Clostridioides difficile (C. diff) are the most commonly identified cause of healthcare-associated infection in the elderly. Risk factors include advanced age, hospitalization, prior or concomitant systemic antibacterial therapy, chemotherapy, and gastrointestinal surgery. Patients with unspecified and new-onset diarrhea with ≥3 unformed stools in 24 h are the target population for C. diff infection (CDI) testing. To present data on the risks of laboratory misdiagnosis in managing CDI. Materials. In two general hospitals, we examined 116 clinical stool specimens from hospitalized patients with acute diarrhea suspected of nosocomial or antibiotic-associated diarrhea (AAD) due to C. diff. Enzyme immunoassay (EIA) tests for the detection of C. diff toxins A (cdtA) and B (cdtB) in stool, automated CLIA assay for the detection of C. diff GDH antigen and qualitative determination of cdtA and B in human feces and anaerobic stool culture were applied for CDI laboratory diagnosis. MALDI-TOF (Bruker) was used to identify the presumptive anaerobic bacterial colonies. The following methods were used as confirmatory diagnostics: the LAMP method for the detection of Salmonella spp. and simultaneous detection of C. jejuni and C. coli, an E. coli Typing RT-PCR detection kit (ETEC, EHEC, STEC, EPEC, and EIEC), API 20E and aerobic stool culture methods. Results. A total of 40 toxigenic strains of C. diff were isolated from all 116 tested diarrheal stool samples, of which 38/40 produced toxin B and 2/40 strains were positive for both cdtA and cdtB. Of the stool samples positive for cdtA (6/50) and/or cdtB (44/50) by EIA, 33 were negative for C. diff culture but positive for the following diarrheal agents: Salmonella enterica subsp. arizonae (1/33, LAMP, culture, API 20E); C. jejuni (2/33, LAMP, culture, MALDI TOF); ETEC O142 (1/33), STEC O145 and O138 (2/33, E. coli RT-PCR detection kit, culture); C. perfringens (2/33, anaerobic culture, MALDI TOF); hypermycotic enterotoxigenic K. pneumonia (2/33) and enterotoxigenic P. mirabilis (2/33, culture; PCR encoding LT-toxin). Two of the sixty-six cdtB-positive samples (2/66) showed a similar misdiagnosis when analyzed using the CLIA method. However, the PCR analysis showed that they were cdtB-negative. In contrast, the LAMP method identified a positive result for C. jejuni in one sample, and another was STEC positive (stx1+/stx2+) by RT-PCR. We found an additional discrepancy in the CDI test results: EPEC O86 (RT-PCR eae+) was isolated from a fecal sample positive for GHA enzyme (CLIA) and negative for cdtA and cdtB (CLIA and PCR). However, the culture of C. diff was negative. These findings support the hypothesis that certain human bacterial pathogens that produce enterotoxins other than C. diff, as well as intestinal commensal microorganisms, including Klebsiella sp. and Proteus sp., contribute to false-positive EIA card tests for C. diff toxins A and B, which are the most widely used laboratory tests for CDI. Conclusions. CDI presents a significant challenge to clinical practice in terms of laboratory diagnostic management. It is recommended that toxin-only EIA tests should not be used as the sole diagnostic tool for CDI but should be limited to detecting toxins A and B. Accurate diagnosis of CDI requires a combination of laboratory diagnostic methods on which proper infection management depends. Full article
(This article belongs to the Section Diagnostic Microbiology and Infectious Disease)
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20 pages, 1663 KiB  
Article
Isolation, Enrichment and Analysis of Aerobic, Anaerobic, Pathogen-Free and Non-Resistant Cellulose-Degrading Microbial Populations from Methanogenic Bioreactor
by Lyudmila Dimitrova, Yana Ilieva, Dilnora Gouliamova, Vesselin Kussovski, Venelin Hubenov, Yordan Georgiev, Tsveta Bratanova, Mila Kaleva, Maya M. Zaharieva and Hristo Najdenski
Genes 2025, 16(5), 551; https://doi.org/10.3390/genes16050551 - 30 Apr 2025
Viewed by 683
Abstract
Background: Nowadays, the microbial degradation of cellulose represents a new perspective for reducing cellulose waste from industry and households and at the same time obtaining energy sources. Methods: We isolated and enriched two aerobic (at 37 °C and 50 °C) and one anaerobic [...] Read more.
Background: Nowadays, the microbial degradation of cellulose represents a new perspective for reducing cellulose waste from industry and households and at the same time obtaining energy sources. Methods: We isolated and enriched two aerobic (at 37 °C and 50 °C) and one anaerobic microbial consortium from an anaerobic bioreactor for biogas production by continuous subculturing on peptone cellulose solution (PCS) medium supplemented with 0.3% treated or untreated Whatman filter paper under static conditions. Samples were taken every 7 days until day 21 to determine the percentage of cellulose biodegradation. We determined the antimicrobial resistance of aerobic and anaerobic consortia and some single colonies by disc diffusion method, against 42 clinically applied antibiotics. PCR analyses were performed to search for the presence of eight genes for cellulolytic activity and nine genes for antibiotic resistance. By metagenomics analysis, the bacterial and fungal genus distributions in the studied populations were determined. Results: Aerobes cultured at 50 °C degraded cellulose to the greatest extent (47%), followed by anaerobes (24–38%) and aerobes (8%) cultured at 37 °C. The bacterial sequence analysis showed that the dominant phyla are Bacillota and Bacteroidetes and genera—Paraclostridium, Defluvitalea, Anaerobacillus, Acetivibrio, Lysinibacillus, Paenibacillus, Romboutsia, Terrisporobacter, Clostridium, Sporanaerobacter, Lentimicrobium, etc. in a different ratio depending on the cultivation conditions and the stage of the process. Some of these representatives are cellulolytic and hemicellulolytic microorganisms. We performed lyophilization and proved that it is suitable for long-term storage of the most active consortium, which degrades even after the 10th re-inoculation for a period of one year. We proved the presence of ssrA, ssrA BS and blaTEM genes. Conclusions: Our findings demonstrated the potential utility of the microbial consortium of anaerobes in the degradation of waste lignocellulose biomass. Full article
(This article belongs to the Section Genes & Environments)
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15 pages, 2149 KiB  
Article
Reference Whole Genome Sequence Analyses and Characterization of a Novel Carnobacterium maltaromaticum Distinct Sequence Type Isolated from a North American Gray Wolf (Canis lupus) Gastrointestinal Tract
by C. Cristoph Klews, Jessika L. Bryant, Jennifer McCabe, Ariel N. Atchley, Thomas W. Cousins, Maya Barnard-Davidson, Mark R. Ackermann, Michael Netherland, Nur A. Hasan, Peter A. Jordan, Evan S. Forsythe, Patrick N. Ball and Bruce S. Seal
Vet. Sci. 2025, 12(5), 410; https://doi.org/10.3390/vetsci12050410 - 27 Apr 2025
Viewed by 995
Abstract
We hypothesize that bacteria isolated from free-ranging animals could potentially be useful for practical applications. To meet this objective a Gram-positive bacterium was isolated from the gastrointestinal (GI) tract of a Gray Wolf (Canis lupus) using Brucella broth with hemin and [...] Read more.
We hypothesize that bacteria isolated from free-ranging animals could potentially be useful for practical applications. To meet this objective a Gram-positive bacterium was isolated from the gastrointestinal (GI) tract of a Gray Wolf (Canis lupus) using Brucella broth with hemin and vitamin K (BBHK). By small ribosomal RNA (16S) gene sequencing the bacterium was initially identified as a novel Carnobacterium maltaromaticum strain. The bacterium could be propagated both anaerobically and aerobically and was both catalase/oxidase negative and negative by the starch hydrolysis as well as negative using lipase assays. The reference whole genome sequence (WGS) was obtained using both Illumina and Nanopore sequencing. The genome assembly was 3,512,202 bp in length, encoding core bacterial genes with a GC% content of 34.48. No lysogenic bacteriophage genes were detected, although the genome harbors genes for the expression of bacteriocin and other secondary metabolites with potential antimicrobial properties. Multilocus sequence typing (MLST), WGS phylogenetics, average nucleotide identity (ANI), and single nucleotide polymorphism (SNP) analyses of the isolate’s genome indicate this bacterium is a newly identified Carnobacterium maltaromaticum sequence type (ST). Members of the Carnobacteria have anti-listeria activities, highlighting their potential functional properties. Consequently, the isolate could be a potential probiotic for canids and this is the first report on an axenic C. maltaromaticum culture from the genus Canis. Full article
(This article belongs to the Section Veterinary Microbiology, Parasitology and Immunology)
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25 pages, 7066 KiB  
Article
Unraveling the Skin Microbiome in Hidradenitis Suppurativa: Implications for Treatment and Disease Progression
by Corina Ioana Cucu, Călin Giurcăneanu, Mara Madalina Mihai, Teodora Andronic, Ioan Ancuta, Mircea Ioan Popa, Ioana Sabina Macovei and Liliana Gabriela Popa
J. Clin. Med. 2025, 14(7), 2424; https://doi.org/10.3390/jcm14072424 - 2 Apr 2025
Viewed by 1109
Abstract
Background: Hidradenitis suppurativa (HS) is a chronic, disabling, and disfiguring inflammatory disease with a complex, incompletely elucidated pathogenesis. The role of skin dysbiosis in the development and progression of HS has not yet been clarified. Methods: We performed an observational, prospective culture-based study [...] Read more.
Background: Hidradenitis suppurativa (HS) is a chronic, disabling, and disfiguring inflammatory disease with a complex, incompletely elucidated pathogenesis. The role of skin dysbiosis in the development and progression of HS has not yet been clarified. Methods: We performed an observational, prospective culture-based study that included 40 HS patients and analyzed the bacterial load and diversity in HS skin lesions, their correlation with disease severity, and several host and environmental factors. Additionally, we investigated the prevalence of antibiotic resistance and determined the resistance profile of bacterial strains isolated from chronic HS lesions. Results: An impressive number and diversity of bacterial strains were isolated from both superficial and deep HS lesions. 201 aerobic and anaerobic bacterial strains were isolated, polymicrobial growth being detected in the majority of samples. The most frequently isolated bacteria were Staphylococcus epidermidis, Staphylococcus aureus, Staphylococcus lugdunensis, Peptoniphilus spp., and Enterococcus faecalis in superficial lesions and Staphylococcus epidermidis, Staphylococcus aureus, and Corynebacterium tuberculostearicum in deep lesions. A significantly higher bacterial density and diversity was found in male patients, regardless of the affected area and in patients with severe HS. The proportion of bacterial strains resistant to antibiotics was lower in our study (8.95%) compared to the previously reported data. Conclusions: Our findings indicate dysbiosis as a key player in the initiation and maintenance of the inflammatory process in HS. Further large-scale, prospective studies are required to comprehensively characterize the microbiological landscape of HS and shed light on its contribution in the pathogenesis of the disease. Full article
(This article belongs to the Special Issue Recent Advances in Acne, Rosacea and Hidradenitis Suppurativa)
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20 pages, 5401 KiB  
Article
Detection of Cereibacter azotoformans-YS02 as a Novel Source of Coenzyme Q10 and Its Metabolic Analysis
by Meijie Song, Qianqian Xu, Rifat Nowshin Raka, Chunhua Yin, Xiaolu Liu and Hai Yan
Antioxidants 2025, 14(4), 429; https://doi.org/10.3390/antiox14040429 - 1 Apr 2025
Viewed by 732
Abstract
Coenzyme Q10 (CoQ10), a high-value-added nutraceutical antioxidant, exhibits an excellent ability to prevent cardiovascular disease. Here, a novel Cereibacter azotoformans strain, designated YS02, was isolated for its ability to produce CoQ10 and genetically characterized by whole genome sequencing (WGS). The CoQ10 biosynthesis and [...] Read more.
Coenzyme Q10 (CoQ10), a high-value-added nutraceutical antioxidant, exhibits an excellent ability to prevent cardiovascular disease. Here, a novel Cereibacter azotoformans strain, designated YS02, was isolated for its ability to produce CoQ10 and genetically characterized by whole genome sequencing (WGS). The CoQ10 biosynthesis and metabolism differences of YS02 under various culture conditions were also systematically investigated. Phylogenetic analysis based on 16 S rRNA genes, along with taxonomic verification using average nucleotide identity (ANI) analysis, confirmed its classification as C. azotoformans. Enzymatic genes dxs, dxr, idi, ubiA, and ubiG were annotated in YS02, which are critical genetic hallmarks for CoQ10 biosynthesis. Under aerobic–dark cultivation, YS02 grows well, and CoQ10 production can reach 201 mg/kg. A total of 542 small-molecule metabolites were identified from YS02 in aerobic–dark and anaerobic–light cultivation via ultra-high performance liquid chromatography–coupled quadrupole orbitrap high-resolution mass spectrometry (UPLC-Q-Exactive Orbitrap MS). Additionally, 40 differential metabolites were screened through multivariate statistical analysis. Metabolic pathway analysis revealed that the biosynthesis of phenylalanine, tyrosine, and tryptophan might be latent factors influencing CoQ10 production discrepancies within YS02 under both cultural modes. These findings represent new insights into the metabolic mechanism of YS02 and underscore its potential as an alternative strain source for industrial CoQ10 production, enriching the existing resources. Full article
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26 pages, 780 KiB  
Article
The Microbiological Background of Medication-Related Osteonecrosis of the Jaw (MRONJ): Clinical Evidence Based on Traditional Culture and Molecular Biological Detection Methods
by Zsanett Kövér, Márió Gajdács, Beáta Polgár, Dóra Szabó and Edit Urbán
Antibiotics 2025, 14(2), 203; https://doi.org/10.3390/antibiotics14020203 - 15 Feb 2025
Viewed by 1376
Abstract
Background: Medication-related osteonecrosis of the jaw (MRONJ) is a common adverse event following antiresorptive treatment, leading to chronic inflammation and exposed, necrotic bone surfaces in the jawbone. There is an increasing recognition of the role of compositional changes in the colonizing members [...] Read more.
Background: Medication-related osteonecrosis of the jaw (MRONJ) is a common adverse event following antiresorptive treatment, leading to chronic inflammation and exposed, necrotic bone surfaces in the jawbone. There is an increasing recognition of the role of compositional changes in the colonizing members of the oral microbiota implicated in triggering and/or maintaining MRONJ. The aim of our study was to characterize the culturable and non-culturable microbiota—with particular focus on Actinomyces spp. and Actinomyces-like organisms (ALOs)—from surgically removed bone samples of MRONJ patients and healthy control subjects. Methods: n = 35 patients (median age: 70 years) in various stages of MRONJ, with a history of receiving oral or intravenous antiresorptive treatment were included in the study. The controls (n = 35; median age: 35 years) consisted of otherwise healthy individuals undergoing tooth extraction. Traditional, quantitative, aerobic, and anaerobic culture, and Actinomyces-specific PCR was performed for all bone samples from patients and controls, while microbiome analyses—based on 16S rRNA sequencing—were carried out in 5-5 randomly selected samples. Mann–Whitney U test, Wilcoxon rank sum test (alpha diversity), and PERMANOVA analysis (beta diversity) were performed. Results: In MRONJ samples, 185 anaerobic isolates, corresponding to 65 different species were identified (vs. 72 isolates, corresponding to 27 different species in the control group). The detection of Actinomyces spp. and ALOs was more common in MRONJ bone samples, based on traditional culture (65.7% vs. 17.1%; p < 0.001) and PCR (82.9% vs. 37.1%; p < 0.001), respectively. The isolation of Fusobacterium spp. (22 vs. 7; p = 0.001), Prevotella spp. (22 vs. 6; p = 0.034), and Gram-positive anaerobic cocci (GPAC) (30 vs. 9; p = 0.016) was significantly more common in MRONJ patient samples. The microbiota of the controls’ bone samples were characterized by a considerable dominance of Streptococcus spp. and Veillonella spp, while the bacterial abundance rates were substantially more heterogeneous in MRONJ bone samples. Notable differences were not observed among the samples related to the abundance of Actinomyces in the bone microbiota. Conclusions: According to the “infection hypothesis”, alterations in the oral microbiome—with Actinomyces and ALOs being the most relevant—may play a key role in the development, aggravation, and progression of MRONJ. The timely detection of Actinomyces in necrotic bone is crucial, as it has important therapeutic implications. Full article
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16 pages, 1200 KiB  
Article
Effect of Isolation Ruminal Yeast from Ruminants on In Vitro Ruminal Fermentation
by Krung Wilachai, Pramote Paengkoum, Nittaya Taethaisong, Pirat Thitisak, Kriengsak Poonsuk, Juan J. Loor and Siwaporn Paengkoum
Vet. Sci. 2025, 12(2), 155; https://doi.org/10.3390/vetsci12020155 - 11 Feb 2025
Cited by 1 | Viewed by 1068
Abstract
In order to obtain high-performing yeast strains from ruminants, it is necessary to select them from species such as beef cattle, dairy cows, goats, and buffalo. A total of 91 isolated yeasts were collected using the standard methods of microbial culture on agar [...] Read more.
In order to obtain high-performing yeast strains from ruminants, it is necessary to select them from species such as beef cattle, dairy cows, goats, and buffalo. A total of 91 isolated yeasts were collected using the standard methods of microbial culture on agar medium followed by streaking on a plate at least three times until pure yeast colonies were formed. The API 20C AUX Kit and sequencing of the D1/D2 domain of the 26S rRNA gene were used to identify the genera Candida spp., namely, C. glabrata (99% identification), C. tropicallis (99%), C. rugosa (98%), and Issatchenkia orientalis (99%). A total of 12 yeast strains (Dc4, 14, 18; Be1, 2, 7; Bu3, 4, 7; and Go10, 16, 19) were chosen for further analyses. The performance criteria included the ability to tolerate pH values between 3.5 and 7.5, total volatile fatty acids (TVFAs, 0, 0.25, 0.5, 1, 2, and 4% of broth medium), anaerobic growth rate, and in vitro gas production efficiency. First, when all strains were grown at pH values between 3.5 and 7.5, Bu3 and Dc18 performed better than the other strains. Second, at a ruminal pH of 6.5 and a TVFA concentration of between 2 and 4% of the broth medium, strain Bu3 was more resistant than the other strains. Under anaerobic conditions, all strains experienced a decline in viable cell counts when compared with those under aerobic conditions. However, compared to strains Dc14, Be1, Be2, Be7, and Bu3, strain Dc18 exhibited more viable cells under anaerobic conditions in broth medium. The response of strain Dc18 did not differ from those of strains Dc4, Bu4, Bu7, or G16. Strains Be7, Bu3, and Dc18 were used for an in vitro fermentation experiment involving incubation for 2, 4, 6, 8, 10, 12, 24, 36, 48, and 72 h. Three ruminal cannulated dairy cows were used as donors of ruminal fluid. The treatments were run in triplicate. The addition of yeast culture had no effect on gas kinetics, gas accumulation, or the ratio of acetic acid and propionic acid, but led to significantly greater butyric acid concentrations at 24 h of incubation. In conclusion, strain Dc18 isolated from dairy cows is suitable for future studies of probiotic yeast development. Full article
(This article belongs to the Special Issue Advancing Ruminant Health and Production: Alternatives to Antibiotics)
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24 pages, 2851 KiB  
Article
Unlocking the Potential of Bacillus subtilis: A Comprehensive Study on Mycotoxin Decontamination, Mechanistic Insights, and Efficacy Assessment in a Liquid Food Model
by Donato Greco, Vito D’Ascanio, Elisa Santovito, Mariagrazia Abbasciano, Laura Quintieri, Clarisse Techer and Giuseppina Avantaggiato
Foods 2025, 14(3), 360; https://doi.org/10.3390/foods14030360 - 22 Jan 2025
Viewed by 2095
Abstract
Mycotoxin detoxification by microorganisms offers a specific, economical, and environmentally sustainable alternative to physical/chemical methods. Three strains of B. subtilis, isolated from poultry farm environments and recognized by EFSA as safe in animal nutrition for all animal species, consumers, and the environment, [...] Read more.
Mycotoxin detoxification by microorganisms offers a specific, economical, and environmentally sustainable alternative to physical/chemical methods. Three strains of B. subtilis, isolated from poultry farm environments and recognized by EFSA as safe in animal nutrition for all animal species, consumers, and the environment, were screened for their ability to remove mycotoxins. All of them demonstrated mycotoxin-dependent removal efficacy, being very effective against ZEA and its analogues (α- and β-ZOL, α- and β-ZAL, and ZAL) achieving up to 100% removal within 24 h under aerobic, anaerobic, and restrictive growth conditions with toxins as the sole carbon source. ZEA removal remained effective across a wide range of pH values (5–8), temperatures (20–40 °C), and at high toxin concentrations (up to 10 µg/mL). Additionally, up to 87% ZEA removal was achieved after 48 h of incubation (30 °C) of the strains in a contaminated liquid food model containing 1 µg/mL of the toxin. Mechanistic studies suggest that ZEA detoxification involves metabolic processes rather than physical adsorption or entrapment into bacterial cells. Enzymatic activities within the bacterial cells or associated with their cell walls likely play a role in the metabolization of the toxin. Interestingly, it has been observed that growth conditions and culture media can influence the metabolization and/or conjugation of the toxin, which can result in the production of various metabolites. Further investigation is needed to identify these metabolites and assess their safety. Full article
(This article belongs to the Special Issue Mycotoxins in Foods: Occurrence, Detection, and Control)
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14 pages, 2051 KiB  
Article
Facultatively Anaerobic Staphylococci Enable Anaerobic Cutibacterium Species to Grow and Form Biofilms Under Aerobic Conditions
by Jeffrey B. Kaplan, Michael Assa, Noor Mruwat, Miloslav Sailer, Suresh Regmi and Khalaf Kridin
Microorganisms 2024, 12(12), 2601; https://doi.org/10.3390/microorganisms12122601 - 16 Dec 2024
Cited by 2 | Viewed by 2260
Abstract
Facultatively anaerobic Staphylococcus spp. and anaerobic Cutibacterium spp. are among the most prominent bacteria on human skin. Although skin microbes generally grow as multispecies biofilms, few studies have investigated the interaction between staphylococci and Cutibacterium spp. in dual-species biofilms. Here, we measured the [...] Read more.
Facultatively anaerobic Staphylococcus spp. and anaerobic Cutibacterium spp. are among the most prominent bacteria on human skin. Although skin microbes generally grow as multispecies biofilms, few studies have investigated the interaction between staphylococci and Cutibacterium spp. in dual-species biofilms. Here, we measured the mono- and dual-species biofilm formation of four staphylococcal species (S. epidermidis, S. hominis, S. capitis, and S. aureus) and two Cutibacterium spp. (C. acnes and C. avidum) cultured in vitro under both aerobic and anaerobic conditions. The biofilms were quantitated by rinsing them to remove planktonic cells, detaching the biofilm bacteria via sonication, and enumerating the cells by dilution plating. When cultured alone, staphylococci formed biofilms under both aerobic and anaerobic conditions, whereas Cutibacterium spp. formed biofilms only under anaerobic conditions. In co-culture, staphylococcal biofilm formation was unaffected by the presence of Cutibacterium spp., regardless of oxygen availability. However, Cutibacterium spp. biofilm formation was significantly enhanced in the presence of staphylococci, enabling robust growth under both anaerobic and aerobic conditions. Fluorescence confocal microscopy of the aerobic dual-species biofilms suggested that staphylococci create anaerobic niches at the base of the biofilm where C. acnes can grow. These findings demonstrate that staphylococci facilitate the colonization of Cutibacterium spp. in oxygen-rich environments, potentially explaining their presence in high numbers on the oxygen-exposed stratum corneum. Full article
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21 pages, 1116 KiB  
Review
Adaptations of Rice Seed Germination to Drought and Hypoxic Conditions: Molecular and Physiological Insights
by Uttam Bahadur Kunwar, Jiancheng Wen, Roshan Subedi, Naresh Singh Bist and Naba Raj Pandit
Seeds 2024, 3(4), 656-676; https://doi.org/10.3390/seeds3040043 - 2 Dec 2024
Cited by 3 | Viewed by 2621
Abstract
Seed germination is crucial for plant survival, crop stand establishment, and achieving optimal grain yield. The main objective of this review is to explore the physiological and molecular mechanisms governing rice seed germination under aerobic (water stress) and anaerobic (hypoxic) conditions in direct-seeded [...] Read more.
Seed germination is crucial for plant survival, crop stand establishment, and achieving optimal grain yield. The main objective of this review is to explore the physiological and molecular mechanisms governing rice seed germination under aerobic (water stress) and anaerobic (hypoxic) conditions in direct-seeded rice (DSR) systems. Moreover, it discusses the recent genomic advancements and innovations to improve rice seed germination. Here, we discuss how coleoptile and mesocotyl elongation plays a vital role in anaerobic germination (AG) and the function of raised antioxidants, including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) in maintaining Reactive Oxygen Species (ROS), and malondialdehyde (MDA) homeostasis for stabilizing seed germination in water-scarce conditions. This study comprehensively highlights the functions and dynamics of phytohormones—GA (gibberellic acid) and ABA (abscisic acid)—key regulatory genes, transcription factors (TFs), key proteins, and regulatory metabolic pathways, including glycolysis, the pentose phosphate pathway (PPP), and the tricarboxylic acid cycle (TCA), in regulating seed germination under both conditions. Conventional agronomic and cultural practices, such as seed selection, seed priming, seed coating, and hardening, have proven to improve seed germination. Moreover, the utilization of molecular and novel approaches—such as clustered regularly interspaced short palindromic repeat (CRISPR-Cas9) mediated genome editing, marker-assisted selection (MAS), genome-wide associations studies (GWAS), single nucleotide polymorphisms (SNPs), multi-omics, RNA sequencing—combined with beneficial quantitative trait loci (QTLs) has expanded knowledge of crop genomics and inheritance. These advancements aid the development of specific traits for enhancing seed germination in DSR. Full article
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12 pages, 1669 KiB  
Article
Dark Anaerobic Conditions Induce a Fast Induction of the Xanthophyll Cycle in Chlamydomonas reinhardtii When Exposed to High Light
by Cecilia Faraloni, Eleftherios Touloupakis and Giuseppe Torzillo
Microorganisms 2024, 12(11), 2264; https://doi.org/10.3390/microorganisms12112264 - 8 Nov 2024
Cited by 3 | Viewed by 1210
Abstract
Background: Dark anaerobiosis promotes the acidification of the thylakoid lumen and a reduction in the plastoquinone (PQ) pool. The relationship between the reduction in the PQ pool in the dark and the induction of the xanthophyll cycle under high light stress was investigated [...] Read more.
Background: Dark anaerobiosis promotes the acidification of the thylakoid lumen and a reduction in the plastoquinone (PQ) pool. The relationship between the reduction in the PQ pool in the dark and the induction of the xanthophyll cycle under high light stress was investigated in Chlamydomonas reinhardtii. Methods: To achieve a comprehensive oxidative/reductive (aerobic/anaerobic conditions) state of the PQ pool, cultures were bubbled with air or nitrogen for 4 h. To induce the xanthophyll cycle, the cultures were then irradiated with 1200 µmolphotons m−2 s−1 white light for 1 h. Results: The anaerobic cultures exhibited a stronger induction of the xanthophyll cycle with a 3.4-fold higher de-epoxidation state than the aerobic cultures. Chlorophyll fluorescence measurements showed that this response was influenced by the previous redox state of the PQ pool, and that dark anaerobiosis triggers physiological responses, such as exposure to high light. Thus, the photosynthetic apparatus in anaerobic cultures was already alerted, at the moment of high light exposure, to give an appropriate response to the stress with a stronger induction of the xanthophyll cycle than in aerobic cultures. Conclusions: Our results provide new information on the importance of the redox signaling pathway and highlight the importance of the reductive conditions of the PQ pool in regulating the physiological responses of photosynthetic organisms to stress. Full article
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