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International Journal of Systematic and... Aug 2019The International Code of Nomenclature of Prokaryotes provides rules that govern the way names are to be selected based on priority of valid publication when two or more...
When treated as heterotypic synonyms the names Caryophanaceae Peshkoff 1939 (Approved Lists 1980) and Caryophanales Peshkoff 1939 (Approved Lists 1980) have priority over the names Planococcaceae Krasil'nikov 1949 (Approved Lists 1980) and Bacillales Prévot 1953 (Approved Lists 1980), respectively.
The International Code of Nomenclature of Prokaryotes provides rules that govern the way names are to be selected based on priority of valid publication when two or more alternatives (synonyms) are available. However, these rules are not always followed. In the case of the name CaryophanaceaePeshkoff 1939 (Approved Lists 1980), when its nomenclatural type CaryophanonPeshkoff 1939 (Approved Lists 1980) is placed in the same taxon as PlanococcusMigula 1894 (Approved Lists 1980), the nomenclatural type of PlanococcaceaeKrasil'nikov 1949 (Approved Lists 1980), then the two are considered to be heterotypic synonyms and the name which has priority is CaryophanaceaePeshkoff 1939 (Approved Lists 1980). Similarly in the case of the name CaryophanalesPeshkoff 1939 (Approved Lists 1980) when its nomenclatural type CaryophanonPeshkoff 1939 (Approved Lists 1980) is placed in the same taxon as Bacillus Cohn 1872 (Approved Lists 1980), the nomenclatural type of BacillalesPrévot 1953 (Approved Lists 1980), then the two are considered to be heterotypic synonyms and the name which has priority is CaryophanalesPeshkoff 1939 (Approved Lists 1980) While the rules of the International Code of Nomenclature of Prokaryotes are unambiguous in determining the correct names despite the fact that the names CaryophanaceaePeshkoff 1939 (Approved Lists 1980) and CaryophanalesPeshkoff 1939 (Approved Lists 1980) are rarely used.
Topics: Bacillales; Phylogeny; Planococcaceae; Terminology as Topic
PubMed: 30896383
DOI: 10.1099/ijsem.0.003354 -
Journal of Applied Microbiology Dec 2022Decomposition, a complicated process, depends on several factors, including carrion insects, bacteria and the environment. However, the composition of and variation in...
AIMS
Decomposition, a complicated process, depends on several factors, including carrion insects, bacteria and the environment. However, the composition of and variation in oral bacteria over long periods of decomposition remain unclear. The current study aims to illustrate the composition of oral bacteria and construct an informative model for estimating the post-mortem interval (PMI) during decomposition.
METHODS AND RESULTS
Samples were collected from rats' oral cavities for 59 days, and 12 time points in the PMI were selected to detect bacterial community structure by sequencing the V3-V4 region of the bacterial 16S ribosomal RNA (16S rRNA) gene on the Ion S5 XL platform. The results indicated that microorganisms in the oral cavity underwent great changes during decomposition, with a tendency for variation to first decrease and then increase at day 24. Additionally, to predict the PMI, an informative model was established using the random forest algorithm. Three genera of bacteria (Atopostipes, Facklamia and Cerasibacillus) were linearly correlated at all 12 time points in the 59-day period. Planococcaceae was selected as the best feature for the last 6 time points. The R of the model reached 93.94%, which suggested high predictive accuracy. Furthermore, to predict the functions of the oral microbiota, PICRUSt results showed that energy metabolism was increased on day 3 post-mortem and carbohydrate metabolism surged significantly on days 3 and 24 post-mortem.
CONCLUSIONS
Overall, our results suggested that post-mortem oral microbial community data can serve as a forensic resource to estimate the PMI over long time periods.
SIGNIFICANCE AND IMPACT OF THE STUDY
The results of the present study are beneficial for estimating the PMI. Identifying changes in the bacterial community is of great significance for further understanding the applicability of oral flora in forensic medicine.
Topics: Rats; Animals; RNA, Ribosomal, 16S; Postmortem Changes; Microbiota; Bacteria; Mouth
PubMed: 35950442
DOI: 10.1111/jam.15771 -
Microorganisms Aug 2022The Tibetan Plateau is regarded as the third pole of the earth and is one of the least explored places on the planet. Tibetan hull-less barley (Hordeum vulgare L. var....
The Tibetan Plateau is regarded as the third pole of the earth and is one of the least explored places on the planet. Tibetan hull-less barley (Hordeum vulgare L. var. nudum) is the only cereal crop grown widely in the Tibetan Plateau as a staple food. Extensive and long-term cropping of barley may influence the soil’s chemical and biological properties, including microbial communities. However, microbiota associated with hull-less barley is largely unexplored. This study aimed to reveal the composition and diversity of bacterial and fungal communities associated with the hull-less barley at different elevations in the Tibetan Plateau. The core bacterial and fungal taxa of Tibetan hull-less barley were identified, with Bacillaceae, Blastocatellaceae, Comamonadaceae, Gemmatimonadaceae, Planococcaceae, Pyrinomonadaceae, Sphingomonadaceae, and Nitrospiraceae being the most abundant bacterial taxa and Ceratobasidiaceae, Chaetomiaceae, Cladosporiaceae, Didymellaceae, Entolomataceae, Microascaceae, Mortierellaceae, and Nectriaceae being the most abundant fungal taxa (relative abundance > 1%). Both bacterial and fungal diversities of hull-less barley were affected by altitude and soil properties such as total carbon, total nitrogen, and available phosphorus and potassium. Both bacterial and fungal diversities showed a significant negative correlation with altitude, indicating that the lower elevations provide a conducive environment for the survival and maintenance of hull-less barley-associated microbiota. Our results also suggest that the high altitude-specific microbial taxa may play an important role in the adaptation of the hull-less barley to the earth’s third pole.
PubMed: 36144339
DOI: 10.3390/microorganisms10091737 -
International Journal of Biological... Oct 2019Oligosaccharides from green algae Ulva lactuca (ULO) and Enteromorpha prolifera (EPO) were used for investigation of anti-ageing effects and the underlying mechanism in...
Oligosaccharides from green algae Ulva lactuca (ULO) and Enteromorpha prolifera (EPO) were used for investigation of anti-ageing effects and the underlying mechanism in SAMP8 mice. The structural properties of ULO and EPO were analyzed by fourier-transform infrared spectroscopy, gas chromatography-mass spectrometry, and agarose gel electrophoresis. These oligosaccharides enhanced the glutathione, superoxide dismutase, catalase, and telomerase levels and total antioxidant capicity, and decreased the levels of malondialdehyde and advanced glycation end products. After ULO and EPO treatment, the levels of inflammatory factors, including IFN-γ, TNF-α, and IL-6, decreased; the BDNF and ChAT levels increased; and hippocampal neurons were protected. Downregulation of the p53 and FOXO1 genes and upregulation of the Sirt1 gene indicated that ULO and EPO have potential therapeutic effects in the prevention of ageing in SAMP8 mice. By 16S rRNA gene high-throughput sequencing, the abundance of Desulfovibrio was discovered to be markedly different in mice treated with ULO and EPO. The abundances of Verrucomicrobiaceae, Odoribacteraceae, Mogibacteriaceae, Planococcaceae, and Coriobacteriaceae were positively correlated with age-related indicators. These results demonstrated that oligosaccharides from U. lactuca and E. prolifera are ideal candidate compounds that can be used in functional foods and pharmaceuticals to prevent ageing.
Topics: Animals; Antioxidants; Aquatic Organisms; Biomarkers; Body Weight; Chlorophyta; Cytokines; Gas Chromatography-Mass Spectrometry; Gastrointestinal Microbiome; Inflammation Mediators; Male; Mice; Neurons; Oligosaccharides; Plant Extracts; RNA, Ribosomal, 16S; Spectroscopy, Fourier Transform Infrared; Sulfates
PubMed: 31377292
DOI: 10.1016/j.ijbiomac.2019.07.195 -
Bioresource Technology Nov 2022Anaerobic digestion of kitchen waste with grass after hyperthermophilic pretreatment was performed in semi-continuously operated reactors. The greatest methane yield of...
Anaerobic digestion of kitchen waste with grass after hyperthermophilic pretreatment was performed in semi-continuously operated reactors. The greatest methane yield of 293 NmlCH/gVS (volatile solids) was reported for the mixture of both substrates at 55 °C with a solids retention time of 30 d and the corresponding organic lading rate of 1.72 kgVS/m/d. In contrast, pretreated grass subjected to thermophilic digestion produced only 131 NmlCH/gVS. However, when mesophilic conditions were applied, the digestion process turned into dark fermentation, especially visible for the mixture. Metagenomic analysis revealed the dominance Ruminococcaceae, Atopobiaceae and Lactobacillaceae at a family level in mesophilic processes, whereas Petrotogaceae, Synergistaceae, Hungateiclostridiaceae, Planococcaceae and two methanogens Methanosarcinaceae and Methanothermobacteriaceae were the most frequent microbes of thermophilic digestion. Kitchen waste can successfully be co-digested with hyperthermophilically pretreated grass at high loading rates, however the digesters must be operated at thermophilic temperatures.
PubMed: 36195216
DOI: 10.1016/j.biortech.2022.128053 -
PloS One 2022The filling mining method is an effective method for controlling ground stress and preventing surface subsidence in the mining field during exploitation of underground...
The filling mining method is an effective method for controlling ground stress and preventing surface subsidence in the mining field during exploitation of underground resources. Tailings can be utilized as the filling material, so as to realize the reuse of industrial waste. However, utilization of the traditional Portland cement as the cementing material for tailings leads to groundwater pollution. In addition, production of Portland cement results in consumption of a great amount of ore and air pollution. In this paper, a tailings cementation method by using the microbial induced calcite precipitation (MICP) technique with immersion curing is proposed. Tailings are cemented by the MICP technique with aerobic bacteria (Sporosarcina pasteurii) under a soaked curing environment. The variable control method is applied to investigate the factors influencing the cementation effects by the MICP technique with Sporosarcina pasteurii, including the bacterial solution concentration, the cementing solution concentration, the particle size of tailings, and the curing temperature. The results indicate that: when OD600 of the Sporosarcina pasteurii solution is 1.6, the urea concentration in the cementing solution is 0.75 mol/L, the tailings are raw materials without grinding, and the curing temperature is 30°C, the cementation effect is the best. In view of uneven calcification during MICP with Sporosarcina pasteurii, mixed Sporosarcina pasteurii and Castellaniella denitrificans are used for tailings cementation. Higher strength of cemented tailings is achieved. It is proved that the MICP technique with mixed aerobic bacteria and facultative anaerobes is an effective method for tailings cementation.
Topics: Bacteria; Calcium Carbonate; Cementation; Immersion; Sporosarcina
PubMed: 35913918
DOI: 10.1371/journal.pone.0272281 -
Hepatology Research : the Official... Dec 2018Cirrhosis is a leading cause of death worldwide, yet there are no well-established risk stratifying tools for lethal complications, including hepatocellular carcinoma...
AIM
Cirrhosis is a leading cause of death worldwide, yet there are no well-established risk stratifying tools for lethal complications, including hepatocellular carcinoma (HCC). Patients with liver cirrhosis undergo routine endoscopic surveillance, providing ready access to duodenal aspirate samples that could be a source for identifying novel biomarkers. The aim of this study was to characterize the microbiome and bile acid profiles in duodenal aspirates from patients with liver cirrhosis to assess the feasibility of developing biomarkers for HCC risk stratification.
METHODS
Thirty patients with liver cirrhosis were enrolled in the Microbiome, Microbial Markers, and Liver Disease study between May 2015 and March 2017. Detailed clinical and epidemiological data were collected at baseline and at 6-monthly follow-up visits. Duodenal aspirate fluid was collected at baseline for microbial characterization using 16S ribosomal RNA sequencing and bile acid quantification using mass spectroscopy.
RESULTS
Alcohol-related cirrhosis was associated with reductions in the Bacteroidetes phylum, particularly Prevotella (13-fold reduction), and expansion of Staphylococcus (13-fold increase), compared to hepatitis C virus-related cirrhosis. Participants with hepatic encephalopathy (HE) had less microbial diversity compared to patients without HE (P < 0.05), and were characterized by expansion of Mycobacterium (45-fold increase) and Gram-positive cocci including Granulicatella (3.1-fold increase), unclassified Planococcaceae (3.3-fold increase), and unclassified Streptococcaceae (4.5-fold increase). Non-Hispanic White patients had reduced microbial richness (P < 0.01) and diversity (P < 0.05), and increased levels of conjugated ursodeoxycholic acid (glycoursodeoxycholic acid and tauroursodeoxycholic acid, P < 0.05) compared to Hispanic patients.
CONCLUSION
Microbial profiles of duodenal aspirates differed by cirrhosis etiology, HE, and Hispanic ethnicity.
PubMed: 29923681
DOI: 10.1111/hepr.13207 -
Bioresource Technology Nov 2021This study aims to construct a high-temperature-resistant microbial consortium to effectively degrade oily food waste by Fed-in-situ biological reduction treatment...
This study aims to construct a high-temperature-resistant microbial consortium to effectively degrade oily food waste by Fed-in-situ biological reduction treatment (FBRT). Oil degrading bacteria were screened under thermophilic conditions of mineral salt medium with increased oil content. The oil degradation and emulsification ability of each stain was evaluated and their synergetic improvement was further confirmed. Consortium of Bacillus tequilensis, Bacillus licheniformis, Bacillus sonorensis and Ureibacillus thermosphaericus was selected and applicated as bacterial agents in FBRT under 55 °C. Changes in pH, moisture, bacterial community and key components of food waste were monitored for 5 days during processing. Facilitated by the bacterial consortium, FBRT gave superior total mass reduction (86.61 ± 0.58% vs. 67.25 ± 1.63%) and non-volatile solids reduction (65.91 ± 1.53% vs. 28.53 ± 2.29%) compared with negative control, the feasibility and efficiency of present FBRT providing a promising in-situ disposal strategy for rapid reduction of oily food waste.
Topics: Bacillus; Biodegradation, Environmental; Food; Microbial Consortia; Planococcaceae; Refuse Disposal; Temperature
PubMed: 34339998
DOI: 10.1016/j.biortech.2021.125635 -
International Microbiology : the... Aug 2021Sabkhas in Kuwait are unique hypersaline marine environments under-explored for bacterial community composition and bioprospecting. The 16S rRNA sequence analysis of 46...
Sabkhas in Kuwait are unique hypersaline marine environments under-explored for bacterial community composition and bioprospecting. The 16S rRNA sequence analysis of 46 isolates with distinct morphology from two Kuwait sabkhas recovered 11 genera. Phylum Firmicutes dominated these isolates, and Bacillus (32.6%) was recovered as the dominant genera, followed by Halococcus (17.4%). These isolates were moderately halophilic, and some of them showed tolerance and growth at extreme levels of salt (20%), pH (5 and/or 11), and temperature (55 °C). A higher percentage of isolates harbored protease (63.0), followed by DNase (41.3), amylase (41.3), and lipase (32.6). Selected isolates showed antimicrobial activity against E. faecalis and isolated Halomonas shengliensis, and Idiomarina piscisalsi harbored gene coding for dNDP-glucose 4,6-dehydratase (Glu 1), indicating their potential to produce biomolecules with deoxysugar moieties. Palmitic acid or oleic acid was the dominant fatty acid, and seven isolates had some polyunsaturated fatty acids (linolenic or γ-linolenic acid). Interestingly, six isolates belonging to Planococcus and Oceanobacillus genus produced squalene, a bioactive isoprenoid molecule. Their content increased 30-50% in the presence of Terbinafine. The potential bioactivities and extreme growth conditions make this untapped bacterial diversity a promising candidate for future bioprospecting studies.
Topics: Anti-Infective Agents; Antineoplastic Agents; Bacillus; Bacteria; Bacterial Proteins; Biodiversity; Bioprospecting; DNA, Bacterial; Enzymes; Fatty Acids; Firmicutes; Geologic Sediments; Halococcus; Kuwait; Phylogeny; Planococcaceae; RNA, Ribosomal, 16S; Salinity; Squalene; Water Microbiology
PubMed: 33755814
DOI: 10.1007/s10123-021-00173-1 -
Microbial Ecology Aug 2022Soil bacterial and fungal communities are suitable soil ecosystem health indicators due to their sensitivity to management practices and their role in soil ecosystem...
Soil bacterial and fungal communities are suitable soil ecosystem health indicators due to their sensitivity to management practices and their role in soil ecosystem processes. Here, information on composition and functions of bacterial and fungal communities were evaluated at two phenological stages of sugarcane (six and twelve months, equivalent to the most intensive vegetative stage and to final maturation, respectively) when organomineral fertilizer, combined with phosphate-solubilizing bacteria (PSB), was added into the soil. Organic compost enriched with apatite (C + A) or phosphorite (C + P) and compost without phosphate enrichment (C) were used in the presence or absence of PSB. In addition, we used a control fertilized with soluble triple superphosphate. The differences were more related to the sampling period than to the type of organomineral fertilizer, being observed higher available phosphorus at six months than at twelve months. Only in the C treatment we observed the presence of Bacillaceae and Planococcaceae, while Pseudomonadaceae were only prevalent in inoculated C + A. As for fungi, the genera Chaetomium and Achroiostachys were only present in inoculated C + P, while the genus Naganishia was most evident in inoculated C + A and in uninoculated C + P. Soliccocozyma represented 75% of the total fungal abundance in uninoculated C while in inoculated C, it represented 45%. The bacterial community was more related to the degradation of easily decomposable organic compounds, while the fungal community was more related to degradation of complex organic compounds. Although the microbial community showed a resilient trait, subtle changes were detected in microbial community composition and function, and this may be related to the increase in yield observed.
Topics: Bacteria; Fertilizers; Microbiota; Phosphates; Saccharum; Soil; Soil Microbiology
PubMed: 34498120
DOI: 10.1007/s00248-021-01855-z