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.

Potential of lactic acid bacteria from Pico cheese for starter culture development

2019 ◽  
Vol 25 (4) ◽  
pp. 303-317 ◽  
Author(s):  
SP Câmara ◽  
A Dapkevicius ◽  
C Riquelme ◽  
RB Elias ◽  
CCG Silva ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Starter Culture ◽  
Fermented Food ◽  
Starter Cultures ◽  
Rrna Gene ◽  
Culture Development ◽  
Positive Traits ◽  
Leuconostoc Pseudomesenteroides ◽  
Cheese Production

Autochthonous lactic acid bacteria may provide a means of promoting the quality and safety of traditional fermented food products, in particular, artisanal cheeses. Pico cheese is an artisanal, dairy specialty of the Azores in risk of disappearing. Efforts to maintain its quality to the requirements of the modern markets are, thus, necessary. Lactic acid bacteria were isolated from artisanal Pico cheese, identified by sequencing of the 16S rRNA gene, and their potential as starter cultures was evaluated by studying their acidification ability, enzymatic activities (caseinolysis, lipolysis and API-ZYM profile), diacetyl and expolysaccharide production, autolysis, antimicrobial activity against Listeria monocytogenes ATCC 7466, Escherichia coli ATCC 25922, Staphylococcus aureus ATCC 29523, Pseudomonas aeruginosa ATCC 27853 and Clostridium perfringens ATCC 8357, sensory evaluation of odour formation in milk, syneresis and firmness of the curd. Several of the studied lactic acid bacteria isolates showed interesting properties for practical application as starters in artisanal cheese production. The isolates with the highest number of positive traits and, therefore, the most promising for starter development were Lactococcus lactis ssp. lactis L1C21M1, Lactobacillus paracasei L1B1E3, Leuconostoc pseudomesenteroides L1C1E6, Lactobacillus casei L1A1E5 and L1C1E8.

Isolation and characterization of bacteriophages infecting Burkholderia glumae, the major causal agent of bacterial panicle blight in rice

Plant Disease ◽  
2021 ◽  
Author(s):  
Nootjarin Jungkhun ◽  
Antonio R. G. Farias ◽  
Inderjit Barphagha ◽  
Sujin - Patarapuwadol ◽  
Jong Hyun Ham
Keyword(s):  
Electron Microscopy ◽  
Foliar Application ◽  
Bacterial Species ◽  
Whole Genome Sequence ◽  
Management Tool ◽  
Whole Genome ◽  
Burkholderia Glumae ◽  
Isolation And Characterization ◽  
Transmission Electron ◽  
Panicle Blight

Bacterial panicle blight (BPB) caused by Burkholderia glumae is one of the most severe seed-borne bacterial diseases of rice in the world, which can decrease rice production by up to 75%. Nevertheless, there are few effective measures to manage this disease. In an attempt to develop an alternative management tool for BPB, we isolated and characterized phages from soil and water that are effective to lyse several strains of B. glumae. After tests of host ranges, the phages NBP1-1, NBP4-7 and NBP4-8 were selected for further comprehensive characterization, all of which could lyse B. glumae BGLa14-8 (phage sensitive) but not B. glumae 336gr-1 (phage insensitive). This result indicates that the phages killing B. glumae cells have specific host ranges at the strain level within the bacterial species. In the greenhouse condition of this study, foliar application of the phage NBP4-7 could reduce the severity of BPB caused by B. glumae BGLa14-8 up to 62%, but did not cause any significant effect on the infection by B. glumae 336gr-1. Electron microscopy and whole-genome sequencing were also performed to characterize the three selected phages. Transmission electron microscopy revealed that the selected phages belong to the family Myoviridae. Furthermore, whole genome sequence analysis indicated that the three phages belong to a same species and are closely related to the Burkholderia phage KL3, a member of the Myoviridae family.

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 Isolation and Characterization of Lactic Acid Bacteria and Yeasts from Typical Bulgarian Sourdoughs

2021 ◽  
Vol 9 (7) ◽  
pp. 1346
Author(s):  
Mariana Petkova ◽  
Petya Stefanova ◽  
Velitchka Gotcheva ◽  
Angel Angelov
Keyword(s):  
Lactic Acid ◽  
Sequence Analysis ◽  
Lactic Acid Bacteria ◽  
Antimicrobial Properties ◽  
Matter Content ◽  
Starter Cultures ◽  
Rrna Gene ◽  
Dry Matter Content ◽  
Isolation And Characterization ◽  
Selection Of

Traditional sourdoughs in Bulgaria were almost extinct during the centralized food production system. However, a rapidly developing trend of sourdough revival in the country is setting the demand for increased production and use of commercial starter cultures. The selection of strains for such cultures is based on geographical specificity and beneficial technological properties. In this connection, the aim of this study was to isolate, identify and characterize lactic acid bacteria (LAB) and yeasts from typical Bulgarian sourdoughs for the selection of strains for commercial sourdough starter cultures. Twelve samples of typical Bulgarian sourdoughs were collected from different geographical locations. All samples were analyzed for pH, total titratable acidity and dry matter content. Enumeration of LAB and yeast was also carried out. Molecular identification by 16S rDNA sequence analysis was performed for 167 LAB isolates, and 106 yeast strains were identified by ITS1-5.8S-ITS2 rRNA gene partial sequence analysis. The LAB strains were characterized according to their amylolytic and proteolytic activity and acidification capacity, and 11 strains were selected for further testing of their antimicrobial properties. The strains with the most pronounced antibacterial and antifungal activity are listed as recommended candidates for the development of starter cultures for sourdoughs or other food products.

Isolation and Characterization of Levoglucosan Metabolizing Bacteria

2021 ◽  
Author(s):  
Ajay S. Arya ◽  
Minh T. H. Hang ◽  
Mark A. Eiteman
Keyword(s):  
Recombinant Expression ◽  
Bacterial Species ◽  
Soluble Carbohydrate ◽  
Rrna Gene ◽  
Gene Products ◽  
16S Rrna Gene Sequences ◽  
E Coli ◽  
Isolation And Characterization ◽  
Charred Wood

Bacteria were isolated from wastewater and soil containing charred wood remnants based on their ability to use levoglucosan as a sole carbon source and on their levoglucosan dehydrogenase (LGDH) activity. On the basis of their 16S rRNA gene sequences, these bacteria represented diverse genera of Microbacterium, Paenibacillus , Shinella , and Klebsiella . Genomic sequencing of the isolates verified that two isolates represented novel species, Paenibacillus athensensis MEC069 T and Shinella sumterensis MEC087 T , while the remaining isolates were closely related to either Microbacterium lacusdiani or Klebsiella pneumoniae . The genetic sequence of LGDH, lgdA , was found in the genomes of these four isolates as well as Pseudarthrobacter phenanthrenivorans Sphe3. The identity of the P. phenanthrenivorans LGDH was experimentally verified following recombinant expression in E. coli . Comparison of the putative genes surrounding lgdA in the isolate genomes indicated that several other gene products facilitate the bacterial catabolism of levoglucosan, including a putative sugar isomerase and several transport proteins. Importance Levoglucosan is the most prevalent soluble carbohydrate remaining after high temperature pyrolysis of lignocellulosic biomass, but it is not fermented by typical production microbes such as Escherichia coli and Saccharomyces cerevisiae . A few fungi metabolize levoglucosan via the enzyme levoglucosan kinase, while several bacteria metabolize levoglucosan via levoglucosan dehydrogenase. This study describes the isolation and characterization of four bacterial species which degrade levoglucosan. Each isolate is shown to contain several genes within an operon involved in levoglucosan degradation, furthering our understanding of bacteria which metabolize levoglucosan.

scholarly journals Whole-Genome Sequence of a Pantoea sp. Strain Isolated from an Olive (Olea europaea L.) Knot

2019 ◽  
Vol 8 (42) ◽  
Author(s):  
Gabriela Vuletin Selak ◽  
Marina Raboteg ◽  
Audrey Dubost ◽  
Danis Abrouk ◽  
Katja Žanić ◽  
...  
Keyword(s):  
Genome Size ◽  
Genome Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Trna Genes ◽  
Whole Genome ◽  
Ribosomal Operon ◽  
Adriatic Coast ◽  
Olive Trees

Here, we present the total genome sequence of Pantoea sp. strain paga, a plant-associated bacterium isolated from knots present on olive trees grown on the Adriatic Coast. The genome size of Pantoea sp. paga is 5.08 Mb, with a G+C content of 54%. The genome contains 4,776 predicted coding DNA sequences (CDSs), including 70 tRNA genes and 1 ribosomal operon. Obtained genome sequence data will provide insight on the physiology, ecology, and evolution of Pantoea spp.

scholarly journals Antimicrobial resistance genetic factor identification from whole-genome sequence data using deep feature selection

2019 ◽  
Vol 20 (S15) ◽  
Author(s):  
Jinhong Shi ◽  
Yan Yan ◽  
Matthew G. Links ◽  
Longhai Li ◽  
Jo-Anne R. Dillon ◽  
...  
Keyword(s):  
Feature Selection ◽  
Antimicrobial Resistance ◽  
Genome Sequence ◽  
Sequence Data ◽  
Bacterial Species ◽  
Clinical Diagnostics ◽  
New Drugs ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data

Abstract Background Antimicrobial resistance (AMR) is a major threat to global public health because it makes standard treatments ineffective and contributes to the spread of infections. It is important to understand AMR’s biological mechanisms for the development of new drugs and more rapid and accurate clinical diagnostics. The increasing availability of whole-genome SNP (single nucleotide polymorphism) information, obtained from whole-genome sequence data, along with AMR profiles provides an opportunity to use feature selection in machine learning to find AMR-associated mutations. This work describes the use of a supervised feature selection approach using deep neural networks to detect AMR-associated genetic factors from whole-genome SNP data. Results The proposed method, DNP-AAP (deep neural pursuit – average activation potential), was tested on a Neisseria gonorrhoeae dataset with paired whole-genome sequence data and resistance profiles to five commonly used antibiotics including penicillin, tetracycline, azithromycin, ciprofloxacin, and cefixime. The results show that DNP-AAP can effectively identify known AMR-associated genes in N. gonorrhoeae, and also provide a list of candidate genomic features (SNPs) that might lead to the discovery of novel AMR determinants. Logistic regression classifiers were built with the identified SNPs and the prediction AUCs (area under the curve) for penicillin, tetracycline, azithromycin, ciprofloxacin, and cefixime were 0.974, 0.969, 0.949, 0.994, and 0.976, respectively. Conclusions DNP-AAP can effectively identify known AMR-associated genes in N. gonorrhoeae. It also provides a list of candidate genes and intergenic regions that might lead to novel AMR factor discovery. More generally, DNP-AAP can be applied to AMR analysis of any bacterial species with genomic variants and phenotype data. It can serve as a useful screening tool for microbiologists to generate genetic candidates for further lab experiments.

scholarly journals Draft Whole-Genome Sequence of Xenorhabdus sp. Strain GDc328, Isolated from the Indigenous South African Nematode Host Steinernema khoisanae

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Lee-Anne O. Soobramoney ◽  
Jonathan Featherston ◽  
Vincent M. Gray
Keyword(s):  
Genome Size ◽  
South African ◽  
Genome Sequence ◽  
Entomopathogenic Nematode ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome

Here, we describe the draft genome sequence of Xenorhabdus sp. GDc328, an endosymbiont of the native South African entomopathogenic nematode host, Steinernema khoisanae . The total genome size of the bacteria is 4.09 Mb. The genome comprises a total of 3,608 genes with a molecular G+C content of 44.64%.

scholarly journals Genome sequence analyses show that Neisseria oralis is the same species as ‘ Neisseria mucosa var. heidelbergensis’

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3920-3926 ◽  
Author(s):  
Julia S. Bennett ◽  
Keith A. Jolley ◽  
Martin C. J. Maiden
Keyword(s):  
Genome Sequence ◽  
Type Species ◽  
Whole Genome Sequence ◽  
23S Rrna ◽  
Rrna Gene ◽  
Whole Genome ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Neisseria Mucosa

Phylogenies generated from whole genome sequence (WGS) data provide definitive means of bacterial isolate characterization for typing and taxonomy. The species status of strains recently defined with conventional taxonomic approaches as representing Neisseria oralis was examined by the analysis of sequences derived from WGS data, specifically: (i) 53 Neisseria ribosomal protein subunit (rps) genes (ribosomal multi-locus sequence typing, rMLST); and (ii) 246 Neisseria core genes (core genome MLST, cgMLST). These data were compared with phylogenies derived from 16S and 23S rRNA gene sequences, demonstrating that the N. oralis strains were monophyletic with strains described previously as representing ‘ Neisseria mucosa var. heidelbergensis’ and that this group was of equivalent taxonomic status to other well-described species of the genus Neisseria . Phylogenetic analyses also indicated that Neisseria sicca and Neisseria macacae should be considered the same species as Neisseria mucosa and that Neisseria flavescens should be considered the same species as Neisseria subflava . Analyses using rMLST showed that some strains currently defined as belonging to the genus Neisseria were more closely related to species belonging to other genera within the family; however, whole genome analysis of a more comprehensive selection of strains from within the family Neisseriaceae would be necessary to confirm this. We suggest that strains previously identified as representing ‘ N. mucosa var. heidelbergensis’ and deposited in culture collections should be renamed N. oralis . Finally, one of the strains of N. oralis was able to ferment lactose, due to the presence of β-galactosidase and lactose permease genes, a characteristic previously thought to be unique to Neisseria lactamica , which therefore cannot be thought of as diagnostic for this species; however, the rMLST and cgMLST analyses confirm that N. oralis is most closely related to N. mucosa .

Sign in / Sign up

Export Citation Format

Share Document