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International Journal of Food Science 2024Indonesia has abundant traditional fermented food with various lactic acid bacteria (LAB), which can be developed into probiotics for pharmaceutical and functional food...
Indonesia has abundant traditional fermented food with various lactic acid bacteria (LAB), which can be developed into probiotics for pharmaceutical and functional food and feed products. This research is aimed at (1) obtaining and identifying LAB isolates and (2) studying the microbiome (bacterial diversity and abundance) of spontaneously-fermented traditional foods of Kalimantan Island, Cincalok, Tempoyak, and Mandai. To obtain LAB isolates, food samples were serially diluted and inoculated on MRS agar that contained 1% CaCO (MRSA). Isolates forming clear zones were purified and identified by DNA barcoding. The microbiome was studied using genomic-sequencing techniques and analysed for taxonomic composition. Seven pure isolates were obtained from Cincalok, two Tempoyak, and one Mandai. DNA barcoding revealed that the Cincalok seven isolates were (strain HSP-S16), (FSB201), , (SS1995), (S11-6), (C01), and (P3.1); two from Tempoyak, (E1D3BL1) and (UMCC-2996); and one from Mandai, (XAAS.x13; non-LAB). The , , , , and belong to LAB. The from Cincalok and non-LAB in these three fermented foods were the first documented report. The microbiome revealed the dominance of phyla in the fermented foods, with 93% in Cincalok, 89.94% in Tempoyak, and 60.32% in Mandai. On the genus level, Cincalok was dominated by 40.33%, 23.29%, 9.27%, and 6.84%. Meanwhile, Tempoyak was dominated only by 89.94%. Mandai were dominated by 31.97%, 17.14%, 16.85%, 15.15%, and 6.2%. However, Mandai's microbiome LAB was not culturable/isolated on MRSA. The plausibility is that those unculturable LAB require coculturing with other bacteria and additional media components to grow on MRSA. This study is the first report regarding the microbiome of Cincalok, Tempoyak, and Mandai, along with their culturable LAB isolates.
PubMed: 38715571
DOI: 10.1155/2024/6589766 -
Pathogens (Basel, Switzerland) Apr 2024A novel coagulase-negative strain (H164) was isolated from soymilk in Taiwan. Comparative sequence analysis of the 16S rRNA gene revealed that the H164 strain is a...
A novel coagulase-negative strain (H164) was isolated from soymilk in Taiwan. Comparative sequence analysis of the 16S rRNA gene revealed that the H164 strain is a member of the genus . We used multilocus sequence analysis (MLSA) and phylogenomic analyses to demonstrate that the novel strain was closely related to , , , and . The average nucleotide identity and digital DNA-DNA hybridization values between H164 and its closest relatives were <95% and <70%, respectively. The H164 strain could also be distinguished from its closest relatives by the fermentation of -fructose, -maltose, -trehalose, and -mannitol, as well as by the activities of α-glucosidase and alkaline phosphatase. The major cellular fatty acids were C15:0 iso and C15:0 anteiso, and the predominant menaquinones were MK-7 and MK-8, respectively. The major cellular fatty acids and predominant menaquinones were C iso and C anteiso and MK-7 and MK-8, respectively. In conclusion, this strain represents a novel species, named sp. nov., with the type strain H164 (=BCRC 81404 = NBRC 116174).
PubMed: 38668298
DOI: 10.3390/pathogens13040343 -
Bioresources and Bioprocessing Jul 2023Proteolysis is the rate-limiting step in the mineralization of organic nitrogen into ammonium (NH) and thereby the ammonia (NH) released during the composting. However,...
Proteolysis is the rate-limiting step in the mineralization of organic nitrogen into ammonium (NH) and thereby the ammonia (NH) released during the composting. However, the dynamics of bacterial proteolytic communities related to NH emissions during the composting systems are mostly unknown. This study aimed to examine and compare the effects of hyperthermophilic pretreatment composting (HPC) and traditional composting (TC) methods on (i) the difference of NH loss and nitrogenous compounds; (ii) the dynamics of the proteolytic bacterial community involved in the proteolysis and (iii) the correlation between the proteolytic bacterial community, biophysiochemical characteristics and NH loss. Results revealed that the HPC decreased NH loss by 42% as compared to TC during 60-day composting period. This was accompanied with an inhibitory effect on protease activity in the HPC where the relative abundances of the proteolytic bacteria (Bacillus megaterium and Staphylococcus cohnii) were reduced significantly as compared to TC. Partial least-squares path modeling suggested that various physicochemical properties such as higher temperature as well as lower C/N ratio during composting played a dominant role in affecting the abundance of proteolytic bacteria, which may have been an important factor contributing to the lower NH loss in HPC. All these findings lead us to conclude that the HPC can significantly reduce NH loss by inhibiting the proteolytic bacteria and protease activity responsible for NH release.
PubMed: 38647615
DOI: 10.1186/s40643-023-00659-y -
Frontiers in Microbiology 2024A comprehensive strategy for microbial identification and contamination investigation during sterile drug manufacturing was innovatively established in this study,...
OBJECTIVE
A comprehensive strategy for microbial identification and contamination investigation during sterile drug manufacturing was innovatively established in this study, mainly based on MALDI-TOF MS for the identification and complemented by sequencing technology on strain typing.
METHODS
It was implemented to monitor the bacterial contamination of a sterile drug manufacturing facility, including its bacterial distribution features and patterns. In three months, two hundred ninety-two samples were collected covering multiple critical components of raw materials, personnel, environment, and production water.
RESULTS
Based on our strategy, the bacterial profile across the production process was determined: 241/292 bacterial identities were obtained, and spp. (40.25%), spp.(11.20%), spp. (8.30%), (5.81%), and spp. (4.56%) are shown to be the most dominant microbial contaminants. With 75.8% species-level and 95.4% genus-level identification capability, MALDI-TOF MS was promising to be a first-line tool for environmental monitoring routine. Furthermore, to determine the source of the most frequently occurring , which evidenced a widespread presence in the entire process, a more discriminating whole-genome SNP typing method was developed to track the transmission routes. Phylogenetic analysis based on SNP results indicated critical environment contamination is highly relevant to personnel flow in this case. The strain typing results provide robust and accurate information for the following risk assessment step and support effective preventive and corrective measures.
CONCLUSION
In general, the strategy presented in this research will facilitate the development of improved production and environmental control processes for the pharmaceutical industry, and give insights about how to provide more sound and reliable evidence for the optimization of its control program.
PubMed: 38410390
DOI: 10.3389/fmicb.2024.1327175 -
Journal of Advanced Veterinary and... Dec 2023This research aims to investigate the microbial diversity of Budu prepared from fresh and frozen fish from the Pariaman and Pasaman districts in West Sumatra Province,...
OBJECTIVE
This research aims to investigate the microbial diversity of Budu prepared from fresh and frozen fish from the Pariaman and Pasaman districts in West Sumatra Province, Indonesia, as well as provide basic information about Budu quality.
MATERIALS AND METHODS
To obtain the bacterial microbial composition, deoxyribonucleic acid extraction was carried out using amplicon-sequencing of the gene in the V3-V4 region from two types of Budu and carried out in duplicate.
RESULTS
Budu prepared with fresh (Pariaman) or frozen (Pasaman) fish was dominated by Firmicutes (78.455%-92.37%) and Proteobacteria (6.477%-7.23%) phyla. The total microbial species in Budu from Pariaman were higher (227 species) than in Pasaman (153 species). The bacterial species found are (1.878%-2.21%), (0.597%-0.70%), (0.00%-0.002%), (0.073%-0.09%), (0.00%-0.01%), (0.00%-0.001%), and (0.00%-0.003%). and are found in both Budu. and are found in Budu Pariaman. and were found in Budu Pasaman.
CONCLUSION
Metagenomic analysis of Budu from different fish, Pariaman (fresh fish) and Pasaman (frozen fish) showed that the biodiversity of bacteria was barely different. Both Budu found lactic acid bacteria from the family, genus and pathogenic bacteria, such as and . The discovery of various species of pathogenic bacteria indicates that development is still needed in the Budu production process to improve Budu quality.
PubMed: 38370893
DOI: 10.5455/javar.2023.j736 -
Medicine Dec 2023To report a case of endophthalmitis in a silicone oil (SO)-filled eye associated with Staphylococcus cohnii. After vitrectomy, the environment for bacterial growth in...
BACKGROUND
To report a case of endophthalmitis in a silicone oil (SO)-filled eye associated with Staphylococcus cohnii. After vitrectomy, the environment for bacterial growth in the eye is removed, and SO has antibacterial effect on a variety of microorganisms. Endophthalmitis is seen in about 0.040% cases after pars plana vitrectomy and is even more uncommon in cases where SO is used.
METHODS
The patient was diagnosed as endophthalmitis and admitted to our hospital for emergency. The main concern is if intraocular infection can be controlled and the visual prognosis. In this case, multiple intravitreal antibiotics injection and anterior chamber washout were performed. Not only that, phacoemulsification was performed.
RESULTS
Hypopyon became less after 3 operations were performed. The infection was under control finally.
CONCLUSION
To the best of our knowledge, it is the first report of S. cohnii endophthalmitis in an SO-filled globe of an middle-aged patient. It is important to treat infective endophthalmitis with antibiotics promptly. Delayed therapy may affect the visual prognosis.
Topics: Middle Aged; Humans; Vitrectomy; Silicone Oils; Endophthalmitis; Anti-Bacterial Agents; Eye Infections, Bacterial; Retrospective Studies
PubMed: 38115335
DOI: 10.1097/MD.0000000000036574 -
Microbiology Resource Announcements Dec 2023We report here the draft genome sequences of ( = 1), ( = 1), ( =1), spp. ( = 5), ( = 3), and isolated from high-touch surfaces in washrooms at a post-secondary...
We report here the draft genome sequences of ( = 1), ( = 1), ( =1), spp. ( = 5), ( = 3), and isolated from high-touch surfaces in washrooms at a post-secondary institution.
PubMed: 37971276
DOI: 10.1128/MRA.00910-23 -
World Journal of Clinical Cases Oct 2023Central venous catheters (CVCs) often cause life-threatening complications, especially CVC-related bloodstream infection (CVC-BSI) and catheter-related thrombosis (CRT)....
BACKGROUND
Central venous catheters (CVCs) often cause life-threatening complications, especially CVC-related bloodstream infection (CVC-BSI) and catheter-related thrombosis (CRT). Here, we report an unusual case of misplaced CVC-induced emphysematous thrombophlebitis, a rare but potentially lethal form of CRT and CVC-BSI characterized by both thrombosis and gas formation.
CASE SUMMARY
A 48-year-old male presented to the emergency room of a local hospital with sudden-onset headache and coma for 4 h. Computed tomography (CT) revealed right basal ganglia hemorrhage, so emergency decompressive craniotomy was performed and a CVC was inserted through the right subclavian vein for fluid resuscitation during anesthesia. Two days later, the patient was transferred to the intensive care unit of our hospital for further critical care. On day 9 after CVC insertion, the patient suddenly developed fever and hypotension. Point-of-care ultrasound (POCUS) demonstrated thrombosis and dilatation of the right internal jugular vein (IJV) filled with thrombosis. Ultrasonography also revealed that the CVC tip had been misplaced into the IJV and was surrounded by gas bubbles, which manifested as hyperechoic lines with dirty shadowing and comet-tail artifacts. Further CT scan confirmed air bubbles surrounding the CVC in the right neck. The final diagnosis was septic emphysematous thrombophlebitis induced by a misplaced CVC and ensuing septic shock. The responsible CVC was removed immediately. The patient received fluid resuscitation, intravenous noradrenaline, and a 10-d ultra-broad spectrum antibiotic treatment to combat septic shock. Both CVC and peripheral venous blood cultures yielded methicillin-resistant . The patient was gradually weaned off vasopressors and the symptoms of redness and swelling in the right neck subsided within 7 d.
CONCLUSION
Emphysematous thrombophlebitis is a fulminant and life-threatening CVC-BSI associated with thrombosis and gas formation in the vein. A misplaced CVC may facilitate the development of emphysematous thrombophlebitis. POCUS can easily identify the artifacts produced by gas and thrombosis, facilitating rapid diagnosis at the bedside.
PubMed: 37946778
DOI: 10.12998/wjcc.v11.i29.7207 -
Frontiers in Cellular and Infection... 2023Patients with spontaneous bacterial peritonitis (SBP) often just receive empirical antibiotic therapy, as pathogens can be identified in only few patients using the...
BACKGROUND
Patients with spontaneous bacterial peritonitis (SBP) often just receive empirical antibiotic therapy, as pathogens can be identified in only few patients using the techniques of conventional culture. Metagenomic next generation sequencing (mNGS) is a useful tool for diagnosis of infectious diseases. However, clinical application of mNGS in diagnosis of infected ascites of cirrhotic patients is rarely reported.
CASE PRESENTATION
A 53-year-old male with cirrhosis on regular hemodialysis presented with continuous abdominal pain. After treatment with empiric antibiotics, his inflammatory parameters decreased without significant relief of abdominal pain. Finally, based on ascites mNGS detection, he was diagnosed as infection of (), a gram-positive opportunistic pathogen. With targeted antibiotic treatment, the bacterial peritonitis was greatly improved and the patient's abdominal pain was significantly alleviated.
CONCLUSIONS
When conventional laboratory diagnostic methods and empirical antibiotic therapy fail, proper application of mNGS can help identify pathogens and significantly improve prognosis and patients' symptoms.
Topics: Male; Humans; Middle Aged; Ascites; High-Throughput Nucleotide Sequencing; Staphylococcal Infections; Anti-Bacterial Agents; Liver Cirrhosis; Peritonitis; Abdominal Pain; Metagenomics; Sensitivity and Specificity
PubMed: 37808911
DOI: 10.3389/fcimb.2023.1240283 -
Journal of Dairy Science Nov 2023Non-aureus staphylococci and the closely related mammaliicoccal species (NASM) are the most common causes of bovine subclinical mastitis on modern dairy farms and are...
Non-aureus staphylococci and the closely related mammaliicoccal species (NASM) are the most common causes of bovine subclinical mastitis on modern dairy farms and are highly prevalent in bulk-tank milk. The purpose of this study was to determine the distribution of NASM in both composite cow milk (CCM) and bulk-tank milk (BTM) samples collected in tandem in commercial Flemish dairy herds and to estimate the origin of the different (subgroups of) NASM species present in BTM by applying strain typing (random amplification of polymorphic DNA or random amplified DNA [RAPD]). A single cross-sectional sampling was performed over 5 herds that volunteered to participate in the study. Composite cow milk samples (n = 356) were collected from all lactating cows (except those with clinical mastitis) during a milking in tandem with 6 BTM samples per herd sequentially collected immediately post that milking (n = 30). In total, 421 and 80 NASM isolates were recovered and identified by MALDI-TOF mass spectrometry from the CCM and BTM samples, respectively and a total of 21 and 12 different NASM species were identified from CCM and BTM samples, respectively. Staphylococcus cohnii was the most prevalent NASM species found in BTM followed by Staphylococcus haemolyticus, Staphylococcus epidermidis, Mammaliicoccus lentus, and Staphylococcus equorum, whereas from CCM samples the most common species were S. hemolyticus, S. cohnii, S. equorum, S. epidermidis, and Staphylococcus chromogenes. The prevalent NASM species in both CCM and BTM samples was distinct for each herd, corroborating other studies observing a herd-specific NASM microbiota. Random amplified DNA analysis was performed on 9 NASM species (S. chromogenes, S. epidermidis, S. haemolyticus, S. equorum, Mammaliicoccus sciuri, Staphylococcus xylosus, S. cohnii, Staphylococcus debuckii, and M. lentus) because these species were isolated from both sample types in a herd. The same RAPD types were found in both sample types for all NASM species selected for strain typing in varying degrees. When assessing the distribution of NASM species, differences within NASM species should be examined meaning a closer look should be taken at the strain level rather than at the species level only.
PubMed: 37641265
DOI: 10.3168/jds.2022-23092