scholarly journals Phylogenetic Framework and Biosurfactant Gene Expression Analysis of Marine Bacillus spp. of Eastern Coastal Plain of Tamil Nadu

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Sreethar Swaathy ◽  
Varadharajan Kavitha ◽  
Arockiasamy Sahaya Pravin ◽  
Ganesan Sekaran ◽  
Asit Baran Mandal ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bacillus Subtilis ◽  
Coastal Plain ◽  
Tamil Nadu ◽  
Bacterial Species ◽  
Individual Species ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
Diversity Assessment ◽  
Bacillus Spp

The present study emphasizes the diversity assessment of marine Bacillus species with special reference to biosurfactant production, respective gene expression, and discrimination among Bacillus licheniformis and Bacillus subtilis. Among the 200 individual species of eastern coastal plain of Tamil Nadu screened, five biosurfactant producing potential bacterial species with entirely different morphology were selected. Biochemical and 16S rRNA gene sequence analysis suggested that all the said five species belong to Bacillus genera but differ in species levels. Biosurfactant of all the five species fluctuates in greater levels with respect to activity as well as to constituents but showed partial similarity to the commercially available surfactin. The expression of srf gene was realized in all of the five species. However, the sfp gene expression was observed only in three species. In conclusion, both B. licheniformis and B. subtilis demonstrate srf gene; nevertheless, sfp gene was expressed only by Bacillus subtilis.

Degradation of zearalenone in swine feed and feed ingredients by Bacillus subtilis ANSB01G

2014 ◽  
Vol 7 (2) ◽  
pp. 143-151 ◽  
Author(s):  
Y.P. Lei ◽  
L.H. Zhao ◽  
Q.G. Ma ◽  
J.Y. Zhang ◽  
T. Zhou ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Culture Supernatant ◽  
Antimicrobial Activities ◽  
Proteinase K ◽  
Rrna Gene ◽  
Distillers Grains With Solubles ◽  
Dried Distillers Grains ◽  
Cell Extracts ◽  
Gene Sequence Analysis ◽  
And Staphylococcus Aureus

Zearalenone (ZEA) and its derivatives are mycotoxins that can cause oestrogenic effects and impair the reproductive physiology of animals, especially in female swine. Strategies to reduce or eliminate ZEA contamination in foods and feeds are very much needed. Among 36 bacterial isolates obtained from a variety of animal intestinal chyme, mouldy foods and feeds, soils, etc., five isolates demonstrated the ability to reduce more than 50% of ZEA in a liquid medium; ANSB01G isolate taken from normal broiler intestinal chyme reduced ZEA the most, by 88.65%. Using physiological, biochemical, and 16S rRNA gene sequence analysis methods, the ANSB01G isolate was identified as Bacillus subtilis. Under simulated intestinal tract conditions, the ANSB01G B. subtilis isolate degraded 84.58, 66.34 and 83.04% of ZEA in naturally contaminated maize, dried distillers’ grains with solubles, and swine complete feed, respectively. The highest degradation of ZEA occurred when the mycotoxin was co-incubated with the whole bacterial culture, resulting in a reduction of 88.65%, followed by 75.60% using culture supernatant, 26.11% using cell extracts, and 15.06% using viable cells. Treatments consisting of both heating and addition of proteinase K significantly reduced the rate of ZEA degradation in the culture supernatant, indicating that the ZEA degradation might be enzymatic. B. subtilis ANSB01G displayed resistance to simulated gastrointestinal tract environments and antimicrobial activities against several common bacterial pathogens, including Escherichia coli, Salmonella typhimurium and Staphylococcus aureus. These properties of B. subtilis ANSB01G suggest the possibility of its potential to effectively degrade ZEA in feed and to develop functional feed products for livestock industries.

Phylogeny and identification of Pantoea species associated with bulb rot and bacterial leaf blight of onion crops in Uruguay

Plant Disease ◽  
2021 ◽  
Author(s):  
Stefanie De Armas ◽  
Guillermo Alesio Galván ◽  
María Inés Lapaz ◽  
Pablo González-Barrios ◽  
Esteban Vicente ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Complex Disease ◽  
Bacterial Species ◽  
Housekeeping Genes ◽  
Leaf Blight ◽  
Rrna Gene ◽  
Breeding Lines ◽  
Gene Sequence Analysis ◽  
Bulb Rot ◽  
Physiological Tests

Onion is among the most consumed vegetables in Uruguay, grown in the Northwestern and Southern regions of the country. The onion supply presents interannual variations associated with significant postharvest losses, mainly caused by bacterial rots. Besides bulb rotting, onion leaf lesions as well as infections on seed-stalks during seed production may be devastating for some varieties under conducive conditions. This research aimed to identify the causal agents of bulb rots and leaf blight of onion crops in Uruguay. Symptomatic bulbs, seeds-stalks and leaves were collected from commercial fields from 2015 to 2020. Bacterial colonies were isolated and identified at genera level using physiological tests and 16S rRNA gene sequence analysis. A collection of 59 Pantoea spp. isolates was obtained (11 from bulbs and 48 from leaves and seeds-stalks). Multilocus sequence analysis (MLSA) using four housekeeping genes (rpoB, gyrB, leuS and fusA) allowed the assignment of the isolates to five Pantoea species: P. ananatis, P. agglomerans, P. allii, P. eucalypti and P. vagans. The last two species were not previously reported as onion pathogens elsewhere. The ability to cause disease symptoms was tested by leaf inoculation and red onion scale assays. Pantoea ananatis isolates showed the highest aggressiveness in both assays. Specific isolates from P. allii (MAI 6022), P. eucalypti (MAI 6036), P. vagans (MAI 6050), and Pantoea sp. (MAI 6049) ranked the second in aggressiveness on onion leaves, while only three isolates belonging to P. eucalypti (MAI 6036 and MAI 6058) and P. agglomerans (MAI 6045) exhibited the same scale clearing phenotype as P. ananatis. Leaf inoculation assays were also performed on a set of eight onion cultivars and breeding lines. Overall, P. ananatis MAI 6032 showed the highest aggressiveness in all tested cultivars, followed by P. eucalypti MAI 6036. The presence of new reported bacterial species leads to complex disease management and highlights the need for further studies on virulence factors and the epidemiology of these pathogens.

scholarly journals Production Optimization and Characterization of Bioactive Compound against Salmonella bacillus subtilis KBB Isolated from Nepal

1970 ◽  
Vol 8 (8) ◽  
pp. 19-29 ◽  
Author(s):  
Dwij Raj Bhatta ◽  
BP Kapadnis
Keyword(s):  
Bacillus Subtilis ◽  
Bioactive Compound ◽  
Multidrug Resistant ◽  
Production Optimization ◽  
Diffusion Method ◽  
Rrna Gene ◽  
Agar Disc ◽  
Bacillus Spp ◽  
One Step ◽  
Potent Antagonist

The present study aimed to isolate bioactive Bacillus spp. against multidrug resistant Salmonella and many other gram-negative bacterial pathogens. Altogether five bioactive Bacillus were isolated from soil samples of Nepal and identified as Bacillus licheniformis, Bacillus subtilis, Bacillus pumilus, Bacillus sp. and Bacillus cereus respectively by conventional techniques and DNA sequencing of the 16S rRNA gene. In all five isolates, the isolate Bacillus subtillis KBB was most potent antagonist of multidrug resistant Salmonella as tested by agar disc diffusion method. The bioactive compound production was optimized and product was purified by TLC, and bioactive molecule was characterized UV, IR NMR and GCMS and identified as peptide compound. Key words: Bacillus; Bioactivity; Production optimization; Peptide compounds; One step solvent extraction; Antibacterial spectrum. DOI: 10.3126/sw.v8i8.3841 Scientific World Vol.8(8) 2010 pp.19-29

scholarly journals Proposal of Lentzea deserti (Okoro et al. 2010) Nouioui et al. 2018 as a later heterotypic synonym of Lentzea atacamensis (Okoro et al. 2010) Nouioui et al. 2018 and an emended description of Lentzea atacamensis

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246533
Author(s):  
Mo Ping ◽  
Zhao Yun-Lin ◽  
Liu Jun ◽  
Gao Jian ◽  
Xu Zheng-Gang
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
Emended Description ◽  
Relationship Of ◽  
Type Strains ◽  
The 16S Rrna Gene

The taxonomic relationship of Lentzea atacamensis and Lentzea deserti were re-evaluated using comparative genome analysis. The 16S rRNA gene sequence analysis indicated that the type strains of L. atacamensis and L. deserti shared 99.7% sequence similarity. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the genomes of two type strains were 88.6% and 98.8%, respectively, greater than the two recognized thresholds values of 70% dDDH and 95–96% ANI for bacterial species delineation. These results suggested that L. atacamensis and L. deserti should share the same taxonomic position. And this conclusion was further supported by similar phenotypic and chemotaxonomic features between them. Therefore, we propose that L. deserti is a later heterotypic synonym of L. atacamensis.

scholarly journals Complementing 16S rRNA Gene Amplicon Sequencing with Total Bacterial Load To Infer Absolute Species Concentrations in the Vaginal Microbiome

mSystems ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
Florencia A. Tettamanti Boshier ◽  
Sujatha Srinivasan ◽  
Anthony Lopez ◽  
Noah G. Hoffman ◽  
Sean Proll ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Relative Abundance ◽  
Bacterial Species ◽  
Bacterial Load ◽  
Amplicon Sequencing ◽  
Individual Species ◽  
Rrna Gene ◽  
Vaginal Microbiome ◽  
Bacterial Concentrations

ABSTRACT Whereas 16S rRNA gene amplicon sequencing quantifies relative abundances of bacterial taxa, variation in total bacterial load between samples restricts its ability to reflect absolute concentrations of individual bacterial species. Quantitative PCR (qPCR) can quantify individual species, but it is not practical to develop a suite of qPCR assays for every bacterium present in a diverse sample. We sought to determine the accuracy of an inferred measure of bacterial concentration using total bacterial load and relative abundance. We analyzed 1,320 samples from 20 women with a history of frequent bacterial vaginosis who self-collected vaginal swabs daily over 60 days. We inferred bacterial concentrations by taking the product of species relative abundance (assessed by 16S rRNA gene amplicon sequencing) and bacterial load (measured by broad-range 16S rRNA gene qPCR). Log10-converted inferred concentrations correlated with targeted qPCR (r = 0. 935, P < 2.2e–16) for seven key bacterial species. The mean inferred concentration error varied across bacteria, with rarer bacteria associated with larger errors. A total of 92% of the >0.5-log10 errors occurred when the relative abundance was <10%. Many errors occurred during early bacterial expansion from or late contraction to low abundance. When the relative abundance of a species is >10%, inferred concentrations are reliable proxies for targeted qPCR in the vaginal microbiome. However, targeted qPCR is required to capture bacteria at low relative abundance and is preferable for characterizing growth and decay kinetics of single species. IMPORTANCE Microbiome studies primarily use 16S rRNA gene amplicon sequencing to assess the relative abundance of bacterial taxa in a community. However, these measurements do not accurately reflect absolute taxon concentrations. We sought to determine whether the product of species’ relative abundance and total bacterial load measured by broad-range qPCR is an accurate proxy for individual species’ concentrations, as measured by taxon-specific qPCR assays. Overall, the inferred bacterial concentrations were a reasonable proxy of species-specific qPCR values, particularly when bacteria are present at a higher relative abundance. This approach offers an opportunity to assess the concentrations of bacterial species and how they change in a community over time without developing individual qPCR assays for each taxon.

scholarly journals Genotyping and Toxigenic Potential of Bacillus subtilis and Bacillus pumilus Strains Occurring in Industrial and Artisanal Cured Sausages

2004 ◽  
Vol 70 (9) ◽  
pp. 5168-5176 ◽  
Author(s):  
Alessandra Matarante ◽  
Federico Baruzzi ◽  
Pier Sandro Cocconcelli ◽  
Maria Morea
Keyword(s):  
Bacillus Subtilis ◽  
Dna Sequences ◽  
Bacillus Pumilus ◽  
Meat Products ◽  
Rrna Gene ◽  
Emerging Pathogens ◽  
Specific Pcr ◽  
Gene Sequence Analysis ◽  
Rapd Pcr ◽  
Cured Meat

ABSTRACT Artisanal and industrial sausages were analyzed for their aerobic, heat-resistant microflora to assess whether new emerging pathogens could be present among Bacillus strains naturally contaminating cured meat products. Sixty-four isolates were characterized by randomly amplified polymorphic DNA (RAPD)-PCR and fluorescent amplified fragment length polymorphism (fAFLP). The biotypes, identified by partial 16S rRNA gene sequence analysis, belonged to Bacillus subtilis, Bacillus pumilus, and Bacillus amyloliquefaciens species. Both RAPD-PCR and fAFLP analyses demonstrated that a high genetic heterogeneity is present in the B. subtilis group even in strains harvested from the same source, making it possible to isolate 56 different biotypes. Moreover, fAFLP analysis made it possible to distinguish B. subtilis from B. pumilus strains. The strains were characterized for their toxigenic potential by molecular, physiological, and immunological techniques. Specific PCR analyses revealed the absence of DNA sequences related to HBL, BcET, NHE, and entFM Bacillus cereus enterotoxins and the enzymes sphingomyelinase Sph and phospholipase PI-PLC in all strains; also, the immunological analyses showed that Bacillus strains did not react with NHE- and HBL-specific antibodies. However, some isolates were found to be positive for hemolytic and lecithinase activity. The absence of toxigenic potential in Bacillus strains from the sausages analyzed indicates that these products can be considered safe under the processing conditions they were produced; however, great care should be taken when the ripening time is shortened, particularly in the case of traditional sausages, which could contain high amounts of Bacillus strains and possibly some B. cereus cells.

scholarly journals Analysis of Bacterial Communities during Clostridium difficile Infection in the Mouse

2015 ◽  
Vol 83 (11) ◽  
pp. 4383-4391 ◽  
Author(s):  
Ekaterina G. Semenyuk ◽  
Valeriy A. Poroyko ◽  
Pehga F. Johnston ◽  
Sara E. Jones ◽  
Katherine L. Knight ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
16S Rrna ◽  
Bacterial Species ◽  
Intestinal Content ◽  
Rrna Gene ◽  
Gi Tract ◽  
Bacterial Populations ◽  
Content Type ◽  
Minority Member ◽  
Gene Sequence Analysis

ABSTRACTClostridium difficileinfection (CDI) is a major cause of health care-associated disease. CDI initiates with ingestion ofC. difficilespores, germination in the gastrointestinal (GI) tract, and then colonization of the large intestine. The interactions betweenC. difficilecells and other bacteria and with host mucosa during CDI remain poorly understood. Here, we addressed the hypothesis that, in a mouse model of CDI,C. difficileresides in multicellular communities (biofilms) in association with host mucosa. To do this, we paraffin embedded and then sectioned the GI tracts of infected mice at various days postinfection (p.i.). We then used fluorescentin situhybridization (FISH) with 16S rRNA probes targeting most bacteria as well asC. difficilespecifically. The results revealed thatC. difficileis present as a minority member of communities in the outer (loose) mucus layer, in the cecum and colon, starting at day 1 p.i. To generate FISH probes that identify bacteria within mucus-associated communities harboringC. difficile, we characterized bacterial populations in the infected mouse GI tract using 16S rRNA gene sequence analysis of bacterial DNA prepared from intestinal content. This analysis revealed the presence of genera of several families belonging toBacteroidetesandFirmicutes. These data suggest that formation of multispecies communities associated with the mucus of the cecum and colon is an important early step in GI tract colonization. They raise the possibility that other bacterial species in these communities modulate the ability ofC. difficileto successfully colonize and, thereby, cause disease.

scholarly journals Thalassolituus oleivorans gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons

2004 ◽  
Vol 54 (1) ◽  
pp. 141-148 ◽  
Author(s):  
Michail M. Yakimov ◽  
Laura Giuliano ◽  
Renata Denaro ◽  
Ermanno Crisafi ◽  
Tatiana N. Chernikova ◽  
...  
Keyword(s):  
Marine Bacterium ◽  
Gene Sequence ◽  
Sea Water ◽  
Enrichment Culture ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Pseudomonas Oleovorans ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

An aerobic, heterotrophic, Gram-negative, curved bacterial strain, designated MIL-1T, was isolated by extinction dilution from an n-tetradecane enrichment culture that was established from sea water/sediment samples collected in the harbour of Milazzo, Italy. In the primary enrichment, the isolate formed creamy-white, medium-sized colonies on the surface of the agar. The isolate did not grow in the absence of NaCl; growth was optimal at 2·7 % NaCl. Only a narrow spectrum of organic compounds, including aliphatic hydrocarbons (C7–C20), their oxidized derivatives and acetate, were used as growth substrates. The isolate was not able to grow under denitrifying conditions. The DNA G+C content and genome size of strain MIL-1T were estimated to be 53·2 mol% and 2·2 Mbp, respectively. The major cellular and phospholipid fatty acids were palmitoleic, palmitic and oleic acids (33·5, 29·5 and 11·0 % and 18, 32 and 31 %, respectively). 3-Hydroxy lauric acid was the only hydroxy fatty acid detected. Thirteen different compounds that belonged to two types of phospholipid (phosphatidylethylamine and phosphatidylglycerol) were identified. 16S rRNA gene sequence analysis revealed that this isolate represents a distinct phyletic lineage within the γ-Proteobacteria and has about 94·4 % sequence similarity to Oceanobacter kriegii (the closest bacterial species with a validly published name). The deduced protein sequence of the putative alkane hydrolase, AlkB, of strain MIL-1T is related to the corresponding enzymes of Alcanivorax borkumensis and Pseudomonas oleovorans (81 and 80 % similarity, respectively). On the basis of the analyses performed, Thalassolituus oleivorans gen. nov., sp. nov. is described. Strain MIL-1T (=DSM 14913T=LMG 21420T) is the type and only strain of T. oleivorans.

scholarly journals Bacillus subtilis Attenuates Hepatic and Intestinal Injuries and Modulates Gut Microbiota and Gene Expression Profiles in Mice Infected with Schistosoma japonicum

2021 ◽  
Vol 9 ◽  
Author(s):  
Datao Lin ◽  
Qiuyue Song ◽  
Yishu Zhang ◽  
Jiahua Liu ◽  
Fang Chen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bacillus Subtilis ◽  
Cell Differentiation ◽  
Gut Microbiota ◽  
Signaling Pathway ◽  
Schistosoma Japonicum ◽  
Expression Profiles ◽  
Parasitic Infection ◽  
Differentially Expressed ◽  
Rrna Gene

Parasitic infection can induce pathological injuries and impact the gut microbiota diversity and composition of the host. Bacillus subtilis is a nonpathogenic and noninvasive probiotic bacterium for humans and other animals, playing an important role in improving the host immune system’s ability to respond to intestinal and liver diseases and modulating gut microbiota. However, whether B. subtilis can impact biological functions in Schistosoma japonicum–infected mice is unclear. This study used oral administration (OA) of B. subtilis to treat mice infected with S. japonicum. We evaluated changes in the gut microbiota of infected mice using 16 S rRNA gene sequencing and differentially expressed gene profiles using transcriptome sequencing after OA B. subtilis. We found that OA B. subtilis significantly attenuated hepatic and intestinal pathological injuries in infected mice. The gut microbiota of mice were significantly altered after S. japonicum infection, while OA B. subtilis remodel the diversity and composition of gut microbiomes of infected mice. We found that the S. japonicum–infected mice with OA B. subtilis had an overabundance of the most prevalent bacterial genera, including Bacteroides, Enterococcus, Lactobacillus, Blautia, Lachnoclostridium, Ruminiclostridium, and Enterobacter. Transcriptomic analysis of intestinal tissues revealed that OA B. subtilis shaped the intestinal microenvironment of the host responding to S. japonicum infection. Differentially expressed genes were classified into KEGG pathways between S. japonicum–infected mice and those without included cell adhesion molecules, intestinal immune network for IgA production, hematopoietic cell lineage, Fc epsilon RI signaling pathway, Th1 and Th2 cell differentiation, Th17 cell differentiation, calcium signaling pathway, Fc gamma R-mediated phagocytosis, chemokine signaling pathway, phospholipase D signaling pathway, NF-kappa B signaling pathway, B cell receptor signaling pathway, pancreatic secretion, and phagosome. In conclusion, our findings showed that OA B. subtilis alleviates pathological injuries and regulates gene expression, implying that B. subtilis supplementation may be a potential therapeutic strategy for schistosomiasis. Our study may highlight the value of probiotics as a beneficial supplementary therapy during human schistosomiasis, but further studies are needed.

scholarly journals Complementing 16S rRNA gene amplicon sequencing with estimates of total bacterial load to infer absolute species concentrations in the vaginal microbiome

2019 ◽  
Author(s):  
Florencia Tettamanti Boshier ◽  
Sujatha Srinivasan ◽  
Anthony Lopez ◽  
Noah G. Hoffman ◽  
Sean Proll ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Vaginosis ◽  
Relative Abundance ◽  
Bacterial Species ◽  
Bacterial Load ◽  
Amplicon Sequencing ◽  
Individual Species ◽  
Rrna Gene ◽  
Associated Bacteria

Whereas 16S rRNA gene amplicon sequencing quantifies relative abundances of bacterial taxa, variation in total bacterial load between samples restricts its ability to reflect absolute concentration of individual species. Quantitative PCR (qPCR) can quantify individual species, but it is not practical to develop a suite of qPCR assays for every bacterium present in a diverse sample. We analyzed 1320 samples from 20 women with a history of frequent bacterial vaginosis, who self-collected vaginal swabs daily over 60 days. We inferred bacterial concentrations by taking the product of species relative abundance (assessed by 16S rRNA gene amplicon sequencing) and total bacterial load (measured by broad-range 16S rRNA gene qPCR). Log10-converted inferred concentrations correlated with targeted qPCR (r = 0. 935, p<2.2e-16) for seven key bacterial species. The mean inferred concentration error varied across bacteria, with rarer bacterial vaginosis-associated bacteria associated with larger errors. 92% of errors >0.5 log10 occurred when relative abundance was <10%. Many errors occurred during early bacterial expansion or late contraction. When relative abundance of a species is >10%, inferred concentrations are reliable proxies for targeted qPCR. However, targeted qPCR is required to capture bacteria at low relative abundance, particularly with BV-associated bacteria during the early onset of bacterial vaginosis.

Sign in / Sign up

Export Citation Format

Share Document