scholarly journals Safety Assessment of a Nham Starter Culture Lactobacillus plantarum BCC9546 via Whole-genome Analysis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Nipa Chokesajjawatee ◽  
Pannita Santiyanont ◽  
Kanittha Chantarasakha ◽  
Kanokarn Kocharin ◽  
Chinae Thammarongtham ◽  
...  
Keyword(s):  
Lactobacillus Plantarum ◽  
Genome Analysis ◽  
Safety Assessment ◽  
Starter Culture ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Microbial Cultures

Abstract The safety of microbial cultures utilized for consumption is vital for public health and should be thoroughly assessed. Although general aspects on the safety assessment of microbial cultures have been suggested, no methodological detail nor procedural guideline have been published. Herein, we propose a detailed protocol on microbial strain safety assessment via whole-genome sequence analysis. A starter culture employed in traditional fermented pork production, nham, namely Lactobacillus plantarum BCC9546, was used as an example. The strain’s whole-genome was sequenced through several next-generation sequencing techniques. Incomplete plasmid information from the PacBio sequencing platform and shorter chromosome size from the hybrid Oxford Nanopore-Illumina platform were noted. The methods for 1) unambiguous species identification using 16S rRNA gene and average nucleotide identity, 2) determination of virulence factors and undesirable genes, 3) determination of antimicrobial resistance properties and their possibility of transfer, and 4) determination of antimicrobial drug production capability of the strain were provided in detail. Applicability of the search tools and limitations of databases were discussed. Finally, a procedural guideline for the safety assessment of microbial strains via whole-genome analysis was proposed.

scholarly journals Phenotypic, Genotypic, and Antimicrobial Characteristics of Streptococcus halichoeri Isolates from Humans, Proposal To Rename Streptococcus halichoeri as Streptococcus halichoeri subsp. halichoeri, and Description of Streptococcus halichoeri subsp. hominis subsp. nov., a Bacterium Associated with Human Clinical Infections

2016 ◽  
Vol 54 (3) ◽  
pp. 739-744 ◽  
Author(s):  
P. L. Shewmaker ◽  
A. M. Whitney ◽  
B. W. Humrighouse
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Sequence Similarity ◽  
Clinical Isolates ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Whole Genome Analysis ◽  
Content Type

Phenotypic, genotypic, and antimicrobial characteristics of six phenotypically distinct human clinical isolates that most closely resembled the type strain ofStreptococcus halichoeriisolated from a seal are presented. Sequencing of the 16S rRNA,rpoB,sodA, andrecNgenes; comparative whole-genome analysis; conventional biochemical and Rapid ID 32 Strep identification methods; and antimicrobial susceptibility testing were performed on the human isolates, the type strain ofS.halichoeri, and type strains of closely related species. The six human clinical isolates were biochemically indistinguishable from each other and showed 100% 16S rRNA,rpoB,sodA, andrecNgene sequence similarity. Comparative 16S rRNA gene sequencing analysis revealed 98.6% similarity toS. halichoeriCCUG 48324T, 97.9% similarity toS. canisATCC 43496T, and 97.8% similarity toS. ictaluriATCC BAA-1300T. A 3,530-bp fragment of therpoBgene was 98.8% similar to theS. halichoeritype strain, 84.6% to theS. canistype strain, and 83.8% to theS.ictaluritype strain. TheS. halichoeritype strain and the human clinical isolates were susceptible to the antimicrobials tested based on CLSI guidelines forStreptococcusspecies viridans group with the exception of tetracycline and erythromycin. The human isolates were phenotypically distinct from the type strain isolated from a seal; comparative whole-genome sequence analysis confirmed that the human isolates wereS. halichoeri. On the basis of these results, a novel subspecies,Streptococcushalichoerisubsp.hominis, is proposed for the human isolates andStreptococcus halichoerisubsp.halichoeriis proposed for the gray seal isolates. The type strain of the novel subspecies is SS1844T= CCUG 67100T= LMG 28801T.

scholarly journals Massilia Cellulosiltytica Sp. Nov., A Novel Cellulose-degrading Bacterium Isolated from Rhizosphere Soil of Rice (Oryza Sativa L.) and whole Genome Analysis

2021 ◽  
Author(s):  
Chuanjiao Du ◽  
Chenxu Li ◽  
Peng Cao ◽  
Tingting Li ◽  
Dandan Du ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Genome Analysis ◽  
Rhizosphere Soil ◽  
Oryza Sativa L ◽  
Rrna Gene ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
North East ◽  
Degrading Bacterium

Abstract A bacterial strain, Gram-stain negative, rod-shaped, aerobic and cellulose-degrading, designated NEAU-DD11T, was isolated from rhizosphere soil of rice collected from Northeast Agricultural University in Harbin, Heilongjiang province, North-east China. Base on 16S rRNA gene sequence analysis, strain NEAU-DD11T belongs to the genus Massilia and shared high sequence similarities with Massilia phosphatilytica 12-OD1T (98.46 %) and Massilia putida 6NM-7T (98.41 %). Phylogenetic analysis based on the 16S rRNA gene and whole genome sequences indicated that strain NEAU-DD11T formed a stable cluster with M. phosphatilytica 12-OD1T and M. putida 6NM-7T. The major fatty acids of the strain were C16:0, C17:0-cyclo and C16:1ω7c. The respiratory quinone was Q-8. The polar lipids profile of the strain showed the presence of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified polar lipid and an unidentified phospholipid. In addition, the digital DNA-DNA hybridization values between strain NEAU-DD11T and M. phosphatilytica 12-OD1T and M. putida 6NM-7T were 45.4% and 35.6%, respectively, which are lower than the accepted threshold value of 70%. The DNA G + C content of strain NEAU-DD11T was 66.2 %. The whole genome analysis showed the strain contained carbohydrate enzymes such as glycoside hydrolase and polysaccharide lyase, which enabled the strain to had the function of degrading cellulose. On the basis of the phenotypic, genotypic and chemotaxonomic characteristics, strain NEAU-DD11T represents a novel species of the genus Massilia, for which the name Massilia cellulosiltytica sp. nov. is proposed. The type strain is NEAU-DD11T (= CCTCC AB 2019141T = DSM 109721T).

scholarly journals Isolation and Characterization of Potential Starter Cultures from the Nigerian Fermented Milk Product nono

2021 ◽  
Vol 9 (3) ◽  
pp. 640
Author(s):  
Olakunle Fagbemigun ◽  
Gyu-Sung Cho ◽  
Niels Rösch ◽  
Erik Brinks ◽  
Katrin Schrader ◽  
...  
Keyword(s):  
Genome Size ◽  
Bacterial Species ◽  
Starter Culture ◽  
Starter Cultures ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Whole Genome ◽  
Milk Product ◽  
Isolation And Characterization ◽  
Culture Development

Nono, an important traditional fermented dairy food produced from cow’s milk in Nigeria, was studied for microbial diversity and for starter culture development for industrial production. On the basis of a polyphasic approach, including phenotypic and genotypic methods such as 16S rRNA gene sequencing, repetitive element PCR (rep-PCR) fingerprinting metagenomics, and whole genome sequencing, we identified Lactobacillus (Lb.) helveticus, Limosilactobacillus (L.) fermentum, Lb. delbrueckii, and Streptococcus (S.) thermophilus as predominant bacterial species involved with milk fermentation during traditional nono production in Nigeria, while the predominant yeast species in nono was identified as Saccharomyces cerevisiae. Using metagenomics, Shigella and potential pathogens such as enterobacteria were detected at low levels of abundance. Strains of the predominant lactic acid bacteria (LAB) were selected for starter cultures combination on the basis of their capacities for rapid growth in milk and reduction of pH below 4.5 and their gelling characteristic, which was demonstrated noticeably only by the S. thermophilus strains. Whole genome sequence analysis of selected bacterial strains showed the largest assembled genome size to be 2,169,635 bp in Lb. helveticus 314, while the smallest genome size was 1,785,639 bp in Lb. delbrueckii 328M. Genes encoding bacteriocins were not detected in all the strains, but all the LAB possessed genes potentially involved in diacetyl production and citrate metabolism. These bacteria isolated from nono can thus be used to improve the microbial safety quality of nono in Nigeria, in addition to improving technological parameters such as gelling viscosity, palatability, and product consistency.

scholarly journals Genomic Analyses of Bifidobacterium moukalabense Reveal Adaptations to Frugivore/Folivore Feeding Behavior

2019 ◽  
Vol 7 (4) ◽  
pp. 99
Author(s):  
Takahiro Segawa ◽  
Satoshi Fukuchi ◽  
Dylan Bodington ◽  
Sayaka Tsuchida ◽  
Pierre Mbehang Nguema ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Gorilla Gorilla ◽  
Rrna Gene ◽  
Whole Genome ◽  
Wild Animals ◽  
Whole Genome Analysis ◽  
Fatty Acid Production ◽  
Two Samples ◽  
Western Lowland Gorillas ◽  
Lowland Gorillas

Despite the essential role of Bifidobacterium in health-promoting gut bacteria in humans, little is known about their functions in wild animals, especially non-human primates. It is difficult to determine in vivo the function of Bifidobacterium in wild animals due to the limited accessibility of studying target animals in natural conditions. However, the genomic characteristics of Bifidobacterium obtained from the feces of wild animals can provide insight into their functionality in the gut. Here, we analyzed the whole genomes of 12 B. moukalabense strains isolated from seven feces samples of wild western lowland gorillas (Gorilla gorilla gorilla), three samples of wild central chimpanzees (Pan troglodytes troglodytes) and two samples of wild forest elephants (Loxodonta cyclotis) in Moukalaba-Doudou National Park, Gabon. In addition, we analyzed the fecal bacterial communities of six wild western lowland gorillas by meta 16S rRNA gene analyses with next generation sequencing. Although the abundance of the genus Bifidobacterium was as low as 0.2% in the total reads, a whole genome analysis of B. moukalabense suggested its contribution digestion of food and nutrition of frugivore/folivore animals. Specifically, the whole genome analysis indicated the involvement of B. moukalabense in hemicellulose degradation for short chain fatty acid production and nucleic acid utilization as nitrogen resources. In comparison with human-associated Bifidobacterium spp., genes for carbohydrate transport and metabolism are not conserved in these wild species. In particular the glycosidases, which are found in all 12 strains of B. moukalabense, were variably detected, or not detected, in human-associated species.

scholarly journals Molecular Epidemiology and Whole-Genome Analysis of Bovine Foamy Virus in Japan

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1017
Author(s):  
Hirohisa Mekata ◽  
Tomohiro Okagawa ◽  
Satoru Konnai ◽  
Takayuki Miyazawa
Keyword(s):  
Phylogenetic Analyses ◽  
Foamy Virus ◽  
Pcr Analysis ◽  
Whole Genome ◽  
Genome Sequences ◽  
Whole Genome Analysis ◽  
Virus Family ◽  
Bovine Foamy Virus ◽  
Novel Genotype

Bovine foamy virus (BFV) is a member of the foamy virus family in cattle. Information on the epidemiology, transmission routes, and whole-genome sequences of BFV is still limited. To understand the characteristics of BFV, this study included a molecular survey in Japan and the determination of the whole-genome sequences of 30 BFV isolates. A total of 30 (3.4%, 30/884) cattle were infected with BFV according to PCR analysis. Cattle less than 48 months old were scarcely infected with this virus, and older animals had a significantly higher rate of infection. To reveal the possibility of vertical transmission, we additionally surveyed 77 pairs of dams and 3-month-old calves in a farm already confirmed to have BFV. We confirmed that one of the calves born from a dam with BFV was infected. Phylogenetic analyses revealed that a novel genotype was spread in Japan. In conclusion, the prevalence of BFV in Japan is relatively low and three genotypes, including a novel genotype, are spread in Japan.

scholarly journals Whole-genome analysis uncovers loss of blaZ associated to carriage isolates belonging to MRSA clone ST5-VI in Cape Verde

2021 ◽  
Author(s):  
Magdalena Wysocka ◽  
Tamar Monteiro ◽  
Carine de Pina ◽  
Deisy Gonçalves ◽  
Sandrine de Pina ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Cape Verde ◽  
Whole Genome ◽  
Whole Genome Analysis
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