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Microorganisms Dec 2019Antibiotic resistance is a global issue which is magnified by interspecies horizontal gene transfer. Understanding antibiotic resistance in bacteria in a natural setting...
Antibiotic resistance is a global issue which is magnified by interspecies horizontal gene transfer. Understanding antibiotic resistance in bacteria in a natural setting is crucial to check whether they are multidrug resistant (MDR) and possibly avoid outbreaks. In this study, we have isolated several antibiotic-resistant bacteria (ARB) ( = 128) from the mangroves in Kerala, India. ARBs were distributed based on antibiotics ( = 1.6 × 10). The 16S rRNA gene characterization revealed dominance by Bacillaceae (45%), Planococcaceae (22.5%), and Enterobacteriaceae (17.5%). A high proportion of the isolates were MDR (75%) with maximum resistance to methicillin (70%). Four isolates affiliated to plant-growth promoters, probiotics, food, and human pathogens were resistant to all antibiotics indicating the seriousness and prevalence of MDR. A significant correlation (R = 0.66; = 2.5 × 10) was observed between MDR and biofilm formation. Antagonist activity was observed in 62.5% isolates. Gram-positive isolates were more susceptible to antagonism (75.86%) than gram-negative (36.36%) isolates. Antagonism interactions against gram-negative isolates were lower (9.42%) when compared to gram-positive isolates (89.85%). Such strong antagonist activity can be harnessed for inspection of novel antimicrobial mechanisms and drugs. Our study shows that MDR with strong biofilm formation is prevalent in natural habitat and if acquired by deadly pathogens may create havoc in public health.
PubMed: 31835720
DOI: 10.3390/microorganisms7120678 -
Frontiers in Veterinary Science 2021The aim of this study was to evaluate the dietary effects of SC06 (SC06) instead of antibiotics on the growth performance, intestinal health, and intestinal microbiota...
The aim of this study was to evaluate the dietary effects of SC06 (SC06) instead of antibiotics on the growth performance, intestinal health, and intestinal microbiota of broilers. A total of 360 30-day-old Lingnan yellow broilers were randomly allocated into two groups with six replicates per group (30 birds per replicate). The broilers were fed either a non-supplemented diet or a diet supplemented with 10 colony-forming units lyophilized SC06 per kilogram feed for 30 days. Results showed that SC06 supplementation had no effect on the growth performance compared with that of the control group. SC06 treatment significantly ( <0.05) increased the total antioxidant capacity (T-AOC), total superoxide dismutase (T-SOD) activity in the liver, and the activities of trypsin, α-amylase (AMS), and NaK-ATPase in the ileum, whereas it decreased ( < 0.05) lipase, gamma glutamyl transpeptidase (γ-GT), and maltase activities in the ileum. Meanwhile, SC06 treatment also improved the immune function indicated by the significantly ( < 0.05) increased anti-inflammatory cytokine [interleukin (IL)-10] level and the decreased ( < 0.05) pro-inflammatory cytokine [IL-6 and tumor necrosis factor (TNF)-α] levels in the ileum. Furthermore, we also found that SC06 enhanced the intestinal epithelial intercellular integrity (tight junction and adhesion belt) in the ileum. Microbial analysis showed that SC06 mainly increased the alpha diversity indices in the jejunum, ileum, and cecum. SC06 treatment also significantly ( < 0.05) increased the abundances of , and in the cecum and simultaneously decreased the abundances of in the duodenum, in the jejunum, and and in cecum. In conclusion, these results suggested that instead of antibiotics showed a potential beneficial effect on the intestinal health of broilers.
PubMed: 34150896
DOI: 10.3389/fvets.2021.679368 -
Journal of Insect Science (Online) 2014The diversity of the intestinal bacterial communities in Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae) larvae and adults was assayed by PCR-DGGE to...
The diversity of the intestinal bacterial communities in Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae) larvae and adults was assayed by PCR-DGGE to determine whether different artificial diets could influence these bacterial communities. Two diets were used for feeding the larvae and four for the adults. Escherichia, Desemzia, Staphylococcus, Asticcacaulis, Cellvibrio, Aurantimonas, and Planomicrobium were isolated from the gut of the adults, with Escherichia and Staphylococcus being the main bacterial communities, and the quantities of intestinal bacterial were different in the adults fed different diets. Specifically, the amount of intestinal bacteria from the adults fed different diets had the following ranking according to the major component of the diet: ant powder > darkling beetle pupa powder > cricket powder > silkworm pupa powder. Escherichia, Bacillus, Staphylococcus, Kurthia, Planococcaceae, Ralstonia, Leptothrix, Acinetobacter, and Pseudomonas were isolated from the gut of the larvae. The quantity of intestinal bacteria from the larvae fed the darkling beetle pupae was greater than that from the larvae fed other artificial diets. This study, for the first time, investigated the effect of artificial diets on the bacterial community and the intestinal microbial diversity of D. helophoroides.
Topics: Animals; Bacteria; Coleoptera; Denaturing Gradient Gel Electrophoresis; Diet; Intestines; Larva; Polymerase Chain Reaction
PubMed: 25199878
DOI: 10.1673/031.014.111 -
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 -
MicrobiologyOpen Jun 2020Strain Y74 was an isolate from the sandy soil in the town of Huatugou, Qinghai-Tibet Plateau, China. An analysis of this strain's phenotypic, chemotaxonomic, and genomic...
Strain Y74 was an isolate from the sandy soil in the town of Huatugou, Qinghai-Tibet Plateau, China. An analysis of this strain's phenotypic, chemotaxonomic, and genomic characteristics established the relationship of the isolate with the genus Planococcus. Strain Y74 was able to grow between 4 and 42°C (with an optimum temperature of 28°C) at pH values of 6-8.5 and in 0%-7% (w/v) NaCl. The dominant quinones were MK-8 and MK-7. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and an unknown phospholipid. The majority of the fatty acid content was anteiso-C (28.8%) followed by C ω7c alcohol (20.9%) and iso-C (13.4%). The 16S rRNA gene sequence similarity analysis demonstrated a stable branch formed by strain Y74 and Planococcus halotolerans SCU63 (99.66%). The digital DNA-DNA hybridization between these two strains was 57.2%. The G + C content in the DNA of Y74 was 44.5 mol%. In addition, the morphological, physiological, and chemotaxonomic pattern clearly differentiated the isolates from their known relatives. In conclusion, the strain Y74 (=JCM 32826 = CICC24461 ) represents a novel member of the genus Planococcus, for which the name Planococcus antioxidans sp. nov. is proposed. Strain Y74 was found to have potent antioxidant activity via its hydrogen peroxide tolerance and its 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging activity. The DPPH radical-scavenging activity was determined to be 40.2 ± 0.7%. The genomic analysis indicated that six peroxidases genes, one superoxide dismutase gene, and one dprA (DNA-protecting protein) are present in the genome of Y74 .
Topics: Antioxidants; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Genome, Bacterial; Planococcus Bacteria; Sequence Analysis, DNA; Soil Microbiology; Tibet; Whole Genome Sequencing
PubMed: 32162498
DOI: 10.1002/mbo3.1028 -
Anais Da Academia Brasileira de Ciencias Mar 2015Two psychrophilic bacterial samples were isolated from King George Island soil, in Antarctica. The phylogenetic analysis based on the 16S rRNA (rrs) gene led to the...
Two psychrophilic bacterial samples were isolated from King George Island soil, in Antarctica. The phylogenetic analysis based on the 16S rRNA (rrs) gene led to the correlation with the closest related isolates as Sporosarcina aquimarina (99%) and Algoriphagus antarcticus (99%), with query coverage of 99% and 98%, respectively. The spent culture media from both isolates displayed proteolytic activities detected by sodium dodecyl sulfate polyacrylamide gel electrophoresis containing gelatin as protein substrate. Under the employed conditions, S. aquimarina showed a 55 kDa protease with the best activity detected at pH 7.0 and at 27°C. A. antarcticus also showed a single extracellular protease, however its molecular mass was around 90kDa and its best activity was detected at pH 9.0 and at 37°C. The proteases from both isolates were inhibited by 1,10-phenanthroline and EDTA, two metalloprotease inhibitors. This is the first record of protease detection in both species, and our results may contribute to broaden the basic knowledge of proteases from the Antarctica environment and may help prospecting future biotechnological applications of these enzymes.
Topics: Antarctic Regions; Bacterial Typing Techniques; Bacteroidetes; Electrophoresis, Polyacrylamide Gel; Molecular Weight; Peptide Hydrolases; Phylogeny; Soil Microbiology; Sporosarcina
PubMed: 25806979
DOI: 10.1590/0001-3765201520130519 -
International Journal of Systematic and... Mar 2024A novel bacterial strain, APC 4016, was previously isolated from the skin of a snub-nosed spiny eel, , from a depth of 1000 m in the northern Atlantic Ocean. Cells...
A novel bacterial strain, APC 4016, was previously isolated from the skin of a snub-nosed spiny eel, , from a depth of 1000 m in the northern Atlantic Ocean. Cells were aerobic, cocci, motile, Gram-positive to Gram-variable staining, and gave rise to orange-pigmented colonies. Growth occurred at 4-40 °C (optimum, 25-28 °C), pH 5.5-12 (optimum, pH 7-7.5), and 0-12 % (w/v) NaCl (optimum, 1 %). 16S rRNA gene phylogenetic analysis confirmed that strain APC 4016 belonged to the genus and was most closely related to IFO 12536 (98.98 % 16S similarity). However, digital DNA-DNA hybridization and average nucleotide identity values between these two strains were low, at 20.1 and 83.8 %, respectively. Major (>10 %) cellular fatty acids of strain APC 4016 were iso-C, anteiso-C and C-ω-Alc. The predominant respiratory quinones were menaquinones 5, 6, 7 and 8. The major cellular polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine, and three unknown lipids were also present. The draft genome sequence is 3.6 Mb with a G+C content of 45.25 mol%. This strain was previously shown to have antimicrobial activity and to encode bacteriocin and secondary metabolite biosynthetic gene clusters. Based on the phylogenetic analysis and its distinct phenotypic characteristics, strain APC 4016 is deemed to represent a novel species of the genus , and for which the name sp. nov. is proposed. The type strain of this species is APC 4016 (=DSM 115753=NCIMB 15463).
Topics: Animals; Fatty Acids; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Base Composition; Bacterial Typing Techniques; DNA, Bacterial; Planococcus Bacteria; Eels
PubMed: 38512752
DOI: 10.1099/ijsem.0.006298 -
PloS One 2021In recent years, Sporosarcina pasteurii (S. pasteurii) has become one of the most popular bacteria in microbially induced calcium carbonate precipitation (MICP). Various...
In recent years, Sporosarcina pasteurii (S. pasteurii) has become one of the most popular bacteria in microbially induced calcium carbonate precipitation (MICP). Various applications have been developed based on the efficient urease that can induce the precipitation of calcium carbonate. However, the metabolic mechanism related to biomineralization of S. pasteurii has not been clearly elucidated. The process of bacterial culture and biomineralization consumes a large amount of urea or ammonium salts, which are usually used as agricultural fertilizers, not to mention probable environmental pollutions caused by the excessive use of these raw materials. Therefore, it is urgent to reveal the mechanism of nitrogen utilization and metabolism of S. pasteurii. In this paper, we compared the growth and gene expression of S. pasteurii under three different culture conditions through transcriptome analyses. GO and KEGG analyses revealed that both ammonium and urea were direct nitrogen sources of S. pasteurii, and the bacteria could not grow normally in the absence of ammonium or urea. To the best of our knowledge, this paper is the first one to reveal the nitrogen utilization mechanism of S. pasteurii through transcriptome methods. Furthermore, the presence of ammonium might promote the synthesis of intracellular ATP and enhance the motility of the bacteria. There should be an ATP synthesis mechanism associated with urea hydrolysis catalyzed by urease in S. pasteurii.
Topics: Adenosine Triphosphate; Ammonium Compounds; Biosynthetic Pathways; Cell Wall; Down-Regulation; Flagella; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Gene Ontology; Genes, Bacterial; Nitrogen; Sporosarcina; Transcriptome; Up-Regulation; Urea; Urease
PubMed: 33561150
DOI: 10.1371/journal.pone.0246818 -
Nucleic Acids Research Apr 2024RNA ligases are important enzymes in molecular biology and are highly useful for the manipulation and analysis of nucleic acids, including adapter ligation in...
RNA ligases are important enzymes in molecular biology and are highly useful for the manipulation and analysis of nucleic acids, including adapter ligation in next-generation sequencing of microRNAs. Thermophilic RNA ligases belonging to the RNA ligase 3 family are gaining attention for their use in molecular biology, for example a thermophilic RNA ligase from Methanobacterium thermoautotrophicum is commercially available for the adenylation of nucleic acids. Here we extensively characterise a newly identified RNA ligase from the thermophilic archaeon Palaeococcus pacificus (PpaRnl). PpaRnl exhibited significant substrate adenylation activity but low ligation activity across a range of oligonucleotide substrates. Mutation of Lys92 in motif I to alanine, resulted in an enzyme that lacked adenylation activity, but demonstrated improved ligation activity with pre-adenylated substrates (ATP-independent ligation). Subsequent structural characterisation revealed that in this mutant enzyme Lys238 was found in two alternate positions for coordination of the phosphate tail of ATP. In contrast mutation of Lys238 in motif V to glycine via structure-guided engineering enhanced ATP-dependent ligation activity via an arginine residue compensating for the absence of Lys238. Ligation activity for both mutations was higher than the wild-type, with activity observed across a range of oligonucleotide substrates with varying sequence and secondary structure.
Topics: RNA Ligase (ATP); Substrate Specificity; Archaeal Proteins; Planococcaceae; Protein Engineering; Mutation; Models, Molecular; Adenosine Triphosphate; Oligonucleotides
PubMed: 38421610
DOI: 10.1093/nar/gkae149 -
PloS One 2018The bacterium Sporosarcina pasteurii can produce significant volumes of solid precipitation in the presence of specific chemical environments. These solid precipitate...
The bacterium Sporosarcina pasteurii can produce significant volumes of solid precipitation in the presence of specific chemical environments. These solid precipitate particles can enter a network of microscale pores and cause long-range clogging. As a result, the medium gains strength and exhibits superior mechanical properties. This concept is also known as Microbiologically Induced Calcite Precipitation (MICP). In this study, we have used sponge blocks as surrogate porous media mimics and analyzed several aspects of MICP. A synergistic approach involving electron microscopy (SEM), computerized X-Ray tomography (μCT), quasi-static compressive load testing and chemical characterization (EDX) has been used to understand several physical and chemical aspects of MICP.
Topics: Calcium Carbonate; Flocculation; Porosity; Sporosarcina
PubMed: 30500841
DOI: 10.1371/journal.pone.0207489