Functional Annotation Genome Unravels Potential Probiotic Bacillus velezensis Strain KMU01 from Traditional Korean Fermented Kimchi

Bacillus velezensis strain KMU01 showing γ-glutamyltransferase activity as a probiotic candidate was isolated from kimchi. However, the genetic information on strain KMU01 was not clear. Therefore, the current investigation was undertaken to prove the probiotic traits of B. velezensis strain KMU01 through genomic analysis. Genomic analysis revealed that strain KMU01 did not encode enterotoxin genes and acquired antibiotic resistance genes. Strain KMU01 genome possessed survivability traits under extreme conditions such as in the presence of gastric acid, as well as several probiotic traits such as intestinal epithelium adhesion and the production of thiamine and essential amino acids. Potential genes for human health enhancement such as those for γ-glutamyltransferase, nattokinase, and bacteriocin production were also identified in the genome. As a starter candidate for food fermentation, the genome of KMU01 encoded for protease, amylase, and lipase genes. The complete genomic sequence of KMU01 will contribute to our understanding of the genetic basis of probiotic properties and allow for the assessment of the effectiveness of this strain as a starter or probiotic for use in the food industry.

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Special Issue: Genetic Basis of Phenotypic Variation in Drosophila and Other Insects

Genes ◽

10.3390/genes12081212 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1212

Author(s):

J. Spencer Johnston ◽

Carl E. Hjelmen

Keyword(s):

Next Generation Sequencing ◽

Genetic Basis ◽

Genomic Sequence ◽

Sequence Data ◽

Complete Genomic Sequence ◽

Special Issue ◽

Model Species ◽

Road Map ◽

Generation Sequencing ◽

Complete Genomic

Next-generation sequencing provides a nearly complete genomic sequence for model and non-model species alike; however, this wealth of sequence data includes no road map [...]

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Phenotypic features and analysis of genes supporting probiotic action unravel underlying perspectives of Bacillus velezensis VTX9 as a potential feed additive for swine

Annals of Microbiology ◽

10.1186/s13213-021-01646-4 ◽

2021 ◽

Vol 71 (1) ◽

Author(s):

Ngoc Tung Quach ◽

Thi Hanh Nguyen Vu ◽

Ngoc Anh Nguyen ◽

Van The Nguyen ◽

Thi Lien Bui ◽

...

Keyword(s):

Pathogenic Bacteria ◽

Genetic Basis ◽

De Novo ◽

Antagonistic Activity ◽

Feed Additives ◽

Feed Additive ◽

Probiotic Properties ◽

Bacillus Velezensis ◽

Phenotypic Analysis ◽

First Time

Abstract Purpose To date, a total of 13 probiotic Bacillus species are considered as a Generally Recognized as Safe organism (GRAS) approved by the US Federal Food, Drug, and Cosmetic Act (FDCA), which are used for food and feed additives. However, Bacillus velezensis is not considered as a probiotic candidate in swine farming due to a lack of genetic basis of probiotic action-related traits. Therefore, the present study was undertaken to exploit the genetic basis underlying the probiotic traits of B. velezensis VTX9. Methods The genome sequencing of B. velezensis VTX9 was performed on a PacBio Sequel platform. The probiotic properties including biosafety, antioxidative capacity, and riboflavin and exopolysaccharide production were evaluated by using genotypic and phenotypic analysis. The secondary metabolite potentials were also predicted. Results Strain VTX9 isolated from swine feces proved some probiotic properties including resistance to 3 mM H2O2, 0.6 mM bile salt, low pH, and antipathogenic activity. The complete genome of B. velezensis VTX9 consists of a 3,985,800 bp chromosome that housed 3736 protein-coding genes and 5 plasmids with the size ranging from 7261 to 20,007 bp. Genome analysis revealed no functional genes encoding enterotoxins and transferable antibiotic resistance, which confirmed the safety of VTX9. A total of 82 genes involved in gastrointestinal stress tolerance were predicted, which has not been reported previously. The maximum production of riboflavin reached 769 ± 7.5 ng/ml in LB medium after 72 h, which was in agreement with the complete de novo riboflavin biosynthetic pathway exploited for the first time in the B. velezensis genome. Antagonistic activity against pathogenic bacteria was attributed to 10 secondary metabolites clusters. The presence of a large gene cluster involved in biosynthesis of exopolysaccharides underscored further the adhesion and biofilm-forming capabilities of VTX9 in swine intestines. Conclusion Our results revealed for the first time that B. velezensis VTX9 has the potential to be a probiotic candidate. The information provided here on the genome of B. velezensis VTX9 opens new opportunities for using B. velezensis as a feed additive for swine farming in the future.

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Genomic features and insights into the biology of Mycoplasma fermentans

Microbiology ◽

10.1099/mic.0.043208-0 ◽

2011 ◽

Vol 157 (3) ◽

pp. 760-773 ◽

Cited By ~ 21

Author(s):

Hagai Rechnitzer ◽

Elzbieta Brzuszkiewicz ◽

Axel Strittmatter ◽

Heiko Liesegang ◽

Inna Lysnyansky ◽

...

Keyword(s):

Genetic Basis ◽

Genomic Sequence ◽

Gene Families ◽

Hypothetical Proteins ◽

Protein Coding ◽

Mycoplasma Fermentans ◽

Coding Sequences ◽

Transporter Family ◽

Genes Encoding ◽

Complete Genomic

We present the complete genomic sequence of Mycoplasma fermentans, an organism suggested to be associated with the pathogenesis of rheumatoid arthritis in humans. The genome is composed of 977 524 bp and has a mean G+C content of 26.95 mol%. There are 835 predicted protein-coding sequences and a mean coding density of 87.6 %. Functions have been assigned to 58.8 % of the predicted protein-coding sequences, while 18.4 % of the proteins are conserved hypothetical proteins and 22.8 % are hypothetical proteins. In addition, there are two complete rRNA operons and 36 tRNA coding sequences. The largest gene families are the ABC transporter family (42 members), and the functionally heterogeneous group of lipoproteins (28 members), which encode the characteristic prokaryotic cysteine ‘lipobox’. Protein secretion occurs through a pathway consisting of SecA, SecD, SecE, SecG, SecY and YidC. Some highly conserved eubacterial proteins, such as GroEL and GroES, are notably absent. The genes encoding DnaK-DnaJ-GrpE and Tig, forming the putative complex of chaperones, are intact, providing the only known control over protein folding. Eighteen nucleases and 17 proteases and peptidases were detected as well as three genes for the thioredoxin-thioreductase system. Overall, this study presents insights into the physiology of M. fermentans, and provides several examples of the genetic basis of systems that might function as virulence factors in this organism.

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Phylogenomic Reconstruction and Metabolic Potential of the Genus Aminobacter

Microorganisms ◽

10.3390/microorganisms9061332 ◽

2021 ◽

Vol 9 (6) ◽

pp. 1332

Author(s):

Irene Artuso ◽

Paolo Turrini ◽

Mattia Pirolo ◽

Gabriele Andrea Lugli ◽

Marco Ventura ◽

...

Keyword(s):

Dna Hybridization ◽

Genetic Basis ◽

Genomic Sequence ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Species Level ◽

Comparative Genomic ◽

Metabolic Potential ◽

Methyl Halides ◽

Terrestrial Environments

Bacteria belonging to the genus Aminobacter are metabolically versatile organisms thriving in both natural and anthropized terrestrial environments. To date, the taxonomy of this genus is poorly defined due to the unavailability of the genomic sequence of A. anthyllidis LMG 26462T and the presence of unclassified Aminobacter strains. Here, we determined the genome sequence of A. anthyllidis LMG 26462T and performed phylogenomic, average nucleotide identity and digital DNA-DNA hybridization analyses of 17 members of genus Aminobacter. Our results indicate that 16S rRNA-based phylogeny does not provide sufficient species-level discrimination, since most of the unclassified Aminobacter strains belong to valid Aminobacter species or are putative new species. Since some members of the genus Aminobacter can utilize certain C1 compounds, such as methylamines and methyl halides, a comparative genomic analysis was performed to characterize the genetic basis of some degradative/assimilative pathways in the whole genus. Our findings suggest that all Aminobacter species are heterotrophic methylotrophs able to generate the methylene tetrahydrofolate intermediate through multiple oxidative pathways of C1 compounds and convey it in the serine cycle. Moreover, all Aminobacter species carry genes implicated in the degradation of phosphonates via the C-P lyase pathway, whereas only A. anthyllidis LMG 26462T contains a symbiosis island implicated in nodulation and nitrogen fixation.

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Technology and Formation Improvement of Consumer Properties of Cold Appetizers from a Silver Carp in the Roll Form

Food Industry ◽

10.29141/2500-1922-2019-4-4-2 ◽

2019 ◽

Vol 4 (4) ◽

pp. 14-22

Author(s):

Olesya Sergeevna ◽

Adelya Bekesheva

Keyword(s):

Fatty Acids ◽

Food Industry ◽

Raw Materials ◽

Silver Carp ◽

Essential Amino Acids ◽

Development Stage ◽

Roll Forming ◽

Fish Gelatin ◽

Organoleptic Characteristics ◽

Food Value

At the present development stage of fish culinary production special significance has range expanding and technology improving for the following purposes: the available fish resources use; the organoleptic characteristics improvement and the nutritional value and competitiveness increase of products manufactured at the enterprises of the food industry. This study concerns the technology and the consumer properties formation improvement of cold appetizers from silver carp in the form of a roll. Unlike traditional the developed products consist of fillet of a bighead silver carp on a skin and an original stuff from egg, vegetables and mushrooms. The researchers conducted study using conventional and special methods. They recommended to introduce gelatin in a dry powdered at the stage of roll forming form in a recipe of the developed fish rolls. A man tested fish gelatin as anew consistency regulator of the developed products. The traditional and fish gelatin use allows to increase the yield of fish cold appetizers in the form of a roll by 8.0 %. When adding gelatin, there was an improvement in consistency and sensory perception of the product as a whole. The analysis results of biological value showed that the developed dishes, being an important additional source of protein and essential amino acids such as threonine, lysine, valine, may well improve the ration balance. The fatty acids ratio in fish rolls prepared according to new recipes is close to the ideal fat in the ratio of saturated, monounsaturated and polyunsaturated fatty acids (35:45:20) and is determined mainly by the composition of fatty acids in silver carp fat. The developed production will allow to expand the range of the food industry enterprises by cold fish appetizers of high quality and food value from available fish raw materials.

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Complete Genomic Sequence of Bacteriophage H188: A Novel Vibrio kanaloae Phage Isolated from Yellow Sea

Current Microbiology ◽

10.1007/s00284-015-0984-6 ◽

2016 ◽

Vol 72 (5) ◽

pp. 628-633 ◽

Cited By ~ 13

Author(s):

Yan Li ◽

Min Wang ◽

Qian Liu ◽

Xue Song ◽

Duobing Wang ◽

...

Keyword(s):

Yellow Sea ◽

Genomic Sequence ◽

Complete Genomic Sequence ◽

Complete Genomic

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Analysis of the complete genomic sequence of HLA-A alleles in the Chinese Han population

International Journal of Immunogenetics ◽

10.1111/j.1744-313x.2009.00874.x ◽

2009 ◽

Vol 36 (6) ◽

pp. 351-360 ◽

Cited By ~ 13

Author(s):

F. Zhu ◽

Y. He ◽

W. Zhang ◽

J. He ◽

...

Keyword(s):

Genomic Sequence ◽

Chinese Han Population ◽

Complete Genomic Sequence ◽

Chinese Han ◽

Han Population ◽

Complete Genomic

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Complete genomic sequence ofKIR3DL1*0150102

Tissue Antigens ◽

10.1111/tan.12458 ◽

2014 ◽

Vol 84 (6) ◽

pp. 595-596

Author(s):

L.-M. Yindom ◽

G. Wong ◽

T. I. de Silva ◽

S. L. Rowland-Jones

Keyword(s):

Genomic Sequence ◽

Complete Genomic Sequence ◽

Complete Genomic

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Cañihua (Chenopodium pallidicaule Aellen) a promising superfood in food industry: a review

Nutrition & Food Science ◽

10.1108/nfs-09-2021-0277 ◽

2021 ◽

Vol ahead-of-print (ahead-of-print) ◽

Author(s):

Jerry Fredy Gomez Cahuata ◽

Yessica Estefany Rosas-Quina ◽

Erika Pachari Vera

Keyword(s):

Food Industry ◽

Unsaturated Fatty Acids ◽

Protein Quality ◽

Current Knowledge ◽

Scientific Information ◽

Essential Amino Acids ◽

High Concentration ◽

Content Type ◽

Functional Value ◽

Potential Applications

Purpose The purpose of this paper is to divulge the current knowledge about the nutritional and functional characteristics of Cañihua (Chenopodium pallidicaule Aellen), in addition to its potential applications in the food industry since research studies related to it are still limited compared to other cereals of greater diffusion. Design/methodology/approach The scientific information was collected from Web of Science, Scopus and Google Scholar databases, using keywords such as nutrition value of Chenopodium pallidicaule, amaranth and pseudocereals. Consistent information was selected according to its relevance, year of publication and accuracy with the topic. A total of 49 research papers were selected. Findings Cañihua is a grain with high nutritional potential, considered a superfood because it has a high protein quality, a balanced composition of essential amino acids and unsaturated fatty acids, with a high concentration of linoleic and oleic acid. Besides, it has a good level of bioactive compounds with high antioxidant capacity. However, its production and consumption are limited outside its area of origin, although its cultivation is possible under harsh conditions. Originality/value This paper, through a systematic bibliographic review, highlights the potential of cañihua to be considered in the development of food products with high nutritional and functional value. The information compiled will help researchers and professionals become aware of the importance of this grain and join forces in its processing and enhancement of its attributes.

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