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TheScientificWorldJournal 2021Lactic acid bacteria (LAB) have long been consumed by people in several fermented foods such as dairy products. A study was conducted on lactating dairy cows to isolate...
Lactic acid bacteria (LAB) have long been consumed by people in several fermented foods such as dairy products. A study was conducted on lactating dairy cows to isolate and characterize LAB from dairy products found in and around Bahir-Dar city, North Western Ethiopia. Milk and milk products were randomly collected from dairy farms, milk vending shops, individual households, and supermarkets for bacteriological investigations. A total of sixteen samples were taken from different sources and cultured on different selective media: de Man, Rogosa, and Sharpe (MRS) agar for spp.; M17 agar for spp.; Rogasa SL agar for spp.; and MRS supplemented with cysteine (0.5%) for spp. Different laboratory techniques were implemented for LAB isolation and identification. A total of 41 bacterial isolates were grouped under five different genera of LAB and spp. were identified based on the growth morphology on the selective media, growth at a different temperature, gas production from glucose, carbohydrate fermentation, and other biochemical tests. LAB genera such as , , , , , and spp. were isolated and identified from raw milk, cheese, and yogurt. Based on the current study, the majority of the LAB (24.38%) was isolated from cheese and yogurt. Among these, , (21.94%), (19.51%), (14.64%), (12.19%), and (7.31%) spp. were also identified from these products. Furthermore, based on the bacterial load count and different identification methodologies, our study revealed that spp. were the dominant LAB isolated from milk and milk products. As a result, since there are few studies on the isolation and identification of lactic acid bacteria from dairy products in Ethiopia, more research studies are needed to complete the identification and characterization to species level and their possible role as probiotics.
Topics: Animals; Bifidobacterium; Cattle; Dairy Products; Dairying; Ethiopia; Female; Lactation; Lactobacillus; Lactococcus; Leuconostoc; Milk; Pediococcus; Streptococcus
PubMed: 34421398
DOI: 10.1155/2021/4697445 -
BMC Genomics Dec 2022Leuconostoc gelidum and Leuconostoc gasicomitatum have dual roles in foods. They may spoil cold-stored packaged foods but can also be beneficial in kimchi fermentation....
BACKGROUND
Leuconostoc gelidum and Leuconostoc gasicomitatum have dual roles in foods. They may spoil cold-stored packaged foods but can also be beneficial in kimchi fermentation. The impact in food science as well as the limited number of publicly available genomes prompted us to create pangenomes and perform genomic taxonomy analyses starting from de novo sequencing of the genomes of 37 L. gelidum/L. gasicomitatum strains from our culture collection. Our aim was also to evaluate the recently proposed change in taxonomy as well as to study the genomes of strains with different lifestyles in foods.
METHODS
We selected as diverse a set of strains as possible in terms of sources, previous genotyping results and geographical distribution, and included also 10 publicly available genomes in our analyses. We studied genomic taxonomy using pairwise average nucleotide identity (ANI) and calculation of digital DNA-DNA hybridisation (dDDH) scores. Phylogeny analyses were done using the core gene set of 1141 single-copy genes and a set of housekeeping genes commonly used for lactic acid bacteria. In addition, the pangenome and core genome sizes as well as some properties, such as acquired antimicrobial resistance (AMR), important due to the growth in foods, were analysed.
RESULTS
Genome relatedness indices and phylogenetic analyses supported the recently suggested classification that restores the taxonomic position of L. gelidum subsp. gasicomitatum back to the species level as L. gasicomitatum. Genome properties, such as size and coding potential, revealed limited intraspecies variation and showed no attribution to the source of isolation. The distribution of the unique genes between species and subspecies was not associated with the previously documented lifestyle in foods. None of the strains carried any acquired AMR genes or genes associated with any known form of virulence.
CONCLUSION
Genome-wide examination of strains confirms that the proposition to restore the taxonomic position of L. gasicomitatum is justified. It further confirms that the distribution and lifestyle of L. gelidum and L. gasicomitatum in foods have not been driven by the evolution of functional and phylogenetic diversification detectable at the genome level.
Topics: Phylogeny; Leuconostoc; DNA; Food Microbiology
PubMed: 36494615
DOI: 10.1186/s12864-022-09032-3 -
Frontiers in Microbiology 2022is a genus of saccharolytic heterofermentative lactic acid bacteria that inhabit plant-derived matrices and a variety of fermented foods (dairy products, dough, milk,...
is a genus of saccharolytic heterofermentative lactic acid bacteria that inhabit plant-derived matrices and a variety of fermented foods (dairy products, dough, milk, vegetables, and meats), contributing to desired fermentation processes or playing a role in food spoilage. At present, the genus encompasses 17 recognized species. In total, 216 deposited genome sequences of were analyzed, to check the delineation of species and to infer their evolutive genealogy utilizing a minimum evolution tree of Average Nucleotide Identity (ANI) and the core genome alignment. Phylogenomic relationships were compared to those obtained from the analysis of 16S rRNA, , and genes. All the phylograms were subjected to split decomposition analysis and their topologies were compared to check the ambiguities in the inferred phylogenesis. The minimum evolution ANI tree exhibited the most similar topology with the core genome tree, while single gene trees were less adherent and provided a weaker phylogenetic signal. In particular, the 16S rRNA gene failed to resolve several bifurcations and species. Based on an ANI threshold of 95%, the organization of the genus could be amended, redefining the boundaries of the species , and . Two strains currently recognized as were split into a separate lineage representing a putative species (G16), phylogenetically related to both (G18) and (G17). Differences among the four subspecies of were not pinpointed by ANI or by the conserved genes. The strains of were ascribed to two putative species, G13 and G14, the former including also all the strains presently belonging to was split into two phylogenetically related lineages, G9 and G10, putatively corresponding to separate species and both including subgroups that may correspond to subspecies. The species and were closely related but separated into different species, the latter including also strains. These results, integrating information of ANI, core genome, and housekeeping genes, complemented the taxonomic delineation with solid information on the phylogenetic lineages evolved within the genus .
PubMed: 35958134
DOI: 10.3389/fmicb.2022.897656 -
Biotechnology Reports (Amsterdam,... Mar 2022Sugarcane deteriorates at a quick rate, just like other perishable crops. The quick loss of sucrose content in sugarcane from the time it is harvested has a significant... (Review)
Review
Sugarcane deteriorates at a quick rate, just like other perishable crops. The quick loss of sucrose content in sugarcane from the time it is harvested has a significant impact on sugar recovery. This problem of post-harvest sucrose losses in sugarcane is a serious concern in cane-producing countries, as it not only leads to low sugar recovery in mills, but also to poor sugar refining. Unreasonable delays in cane transportation from the fields to the mill are frequently linked to a number of problems related to primary or secondary sucrose losses, all of which contribute to a significant reduction in cane weight and sugar recovery. In sugar mills, the processing of damaged or stale canes also presents a number of challenges, including increased viscosity due to dextran generation, formation of acetic acid, and dextrans due to spp. invasion, and so on. The combination of all of these variables results in low sugar quality, resulting in significant losses for sugar mills. The primary and secondary losses caused by post-harvest sucrose degradation in sugarcane are enlisted. The employment of physico-chemical technologies in farmers' fields and sugar mills to control and minimize these losses has also been demonstrated.
PubMed: 35145888
DOI: 10.1016/j.btre.2022.e00705 -
EFSA Journal. European Food Safety... Jan 2023The impact of dry-ageing of beef and wet-ageing of beef, pork and lamb on microbiological hazards and spoilage bacteria was examined and current practices are described....
The impact of dry-ageing of beef and wet-ageing of beef, pork and lamb on microbiological hazards and spoilage bacteria was examined and current practices are described. As 'standard fresh' and wet-aged meat use similar processes these were differentiated based on duration. In addition to a description of the different stages, data were collated on key parameters (time, temperature, pH and a) using a literature survey and questionnaires. The microbiological hazards that may be present in all aged meats included Shiga toxin-producing (STEC), spp., , , enterotoxigenic spp., spp. and spp. Moulds, such as spp. and spp., may produce mycotoxins when conditions are favourable but may be prevented by ensuring a meat surface temperature of -0.5 to 3.0°C, with a relative humidity (RH) of 75-85% and an airflow of 0.2-0.5 m/s for up to 35 days. The main meat spoilage bacteria include spp, spp. spp., spp., spp., spp., spp., spp. and spp. Under current practices, the ageing of meat may have an impact on the load of microbiological hazards and spoilage bacteria as compared to standard fresh meat preparation. Ageing under defined and controlled conditions can achieve the same or lower loads of microbiological hazards and spoilage bacteria than the variable log increases predicted during standard fresh meat preparation. An approach was used to establish the conditions of time and temperature that would achieve similar or lower levels of and (pork only) and lactic acid bacteria (representing spoilage bacteria) as compared to standard fresh meat. Finally, additional control activities were identified that would further assure the microbial safety of dry-aged beef, based on recommended best practice and the outputs of the equivalence assessment.
PubMed: 36698487
DOI: 10.2903/j.efsa.2023.7745 -
Frontiers in Microbiology 2020is a known colonizer of meat-related food matrices. It reaches remarkably high loads during the shelf life in packaged meat products and plays a role in spoilage,...
is a known colonizer of meat-related food matrices. It reaches remarkably high loads during the shelf life in packaged meat products and plays a role in spoilage, although preservative effects have been proposed for some strains. In this study, the draft genomes of 17 strains of (i.e., all the strains that have been sequenced so far) were compared to decipher their metabolic and functional potential and to determine their role in food transformations. Genome comparison and pathway reconstruction indicated that m is a compact group of closely related heterofermentative bacteria sharing most of the metabolic features. Adaptation to a nitrogen-rich environment, such as meat, is evidenced by 23 peptidase genes identified in the core genome and by the autotrophy for nitrogen compounds including several amino acids, vitamins, and cofactors. Genes encoding the decarboxylases yielding biogenic amines were not present. All the strains harbored 1-4 of 32 different plasmids, bearing functions associated to proteins hydrolysis, transport of amino acids and oligopeptides, exopolysaccharides, and various resistances (e.g., to environmental stresses, bacteriophages, and heavy metals). Functions associated to bacteriocin synthesis, secretion, and immunity were also found in plasmids. While genes for lactococcin were found in most plasmids, only three harbored the genes for leucocin B, a class IIa antilisterial bacteriocin. Determinants of antibiotic resistances were absent in both plasmids and chromosomes.
PubMed: 33505375
DOI: 10.3389/fmicb.2020.605127 -
Frontiers in Physiology 2023The short lifespan of enables the efficient investigation of probiotic interventions affecting stress and longevity involving the potential therapeutic value of and...
The short lifespan of enables the efficient investigation of probiotic interventions affecting stress and longevity involving the potential therapeutic value of and isolated from organic basil. The lactic acid bacteria were cultured from the produce collected from a local grocery store in Tulsa, Oklahoma, and then identified through 16S rDNA sequencing and biochemical tests. To dive deep into this analysis for potential probiotic therapy, we used fluorescent reporters that allow us to assess the differential induction of multiple stress pathways such as oxidative stress and the cytoplasmic, endoplasmic reticulum, and the mitochondrial unfolded protein response. This is combined with the classic health span measurements of survival, development, and fecundity, allowing a wide range of organismal observations of the different communities of microbes supported by probiotic supplementation with and . These strains were initially assessed in relation to the feeding strain OP50 and the microbiome. The supplementation showed a reduction in the median lifespan of the worms colonized within the microbiome. This was unsurprising, as negative results are common when probiotics are introduced into healthy microbiomes. To further assess the supplementation potential of these strains on an unhealthy (undifferentiated) microbiome, the typical axenic diet, OP50, was used to simulate this single-species biome. The addition of lactic acid bacteria to OP50 led to a significant improvement in the median and overall survival in simulated biomes, indicating their potential in probiotic therapy. The study analyzed the supplemented cultures in terms of ' morphology, locomotor behavior, reproduction, and stress responses, revealing unique characteristics and stress response patterns for each group. As the microbiome's influence on the health span gains interest, the study aims to understand the microbiome relationships that result in differential stress resistance and lifespans by supplementing microbiomes with and isolated from organic basil in .
PubMed: 37772058
DOI: 10.3389/fphys.2023.1207705 -
Journal of Microbiology and... Jul 2020This study was focused on developing and obtaining a kimchi starter for use in commercial kimchi production. Kimchi varieties made with selected starters are of high...
This study was focused on developing and obtaining a kimchi starter for use in commercial kimchi production. Kimchi varieties made with selected starters are of high quality, have high levels of mannitol, and extended shelf life. The starters were screened for properties such as mannitol production, low gas/acid production, and acid resistance. Finally, kimchi fermentation testing was performed using selected LAB starters. Kimchi samples were prepared with lactic acid bacteria (LAB) starters, including PBio03 and PBio104. The LAB starters are isolated from kimchi and can grow under pH 3.0 and low temperature conditions of 5°C. Four kimchi samples were fermented and stored for 28 days at 5°C. The kimchi samples made with starters (PBio03 and PBio104) had better quality (production of mannitol and maintenance of heterofermentative LAB dominance) than the non-starter kimchi samples. In the starter kimchi, was the dominant LAB, comprising 80% and 70% of total LAB counts at 7 and 21 days, respectively. Mannitol content of the kimchi with PBio03 was 1,423 ± 19.1 mg/ 100 g at 28 days, which was higher than that of the non-starter kimchi sample (1,027 ± 12.2 mg/100 g). These results show the possibility of producing kimchi with improved qualities using PBio03 and PBio104 as starters.
Topics: DNA, Bacterial; Fermentation; Fermented Foods; Food Microbiology; Hydrogen-Ion Concentration; Lactobacillales; Leuconostoc mesenteroides; Mannitol; Taste
PubMed: 32270659
DOI: 10.4014/jmb.2001.01011 -
Food Science and Biotechnology Jun 2021Three bacteriophages (phage), ΦWC53, ΦWC54, and ΦWC56, of were isolated from watery kimchi and characterized. ΦWC53 belonged to Siphoviridae and ΦWC54 and ΦWC56...
Three bacteriophages (phage), ΦWC53, ΦWC54, and ΦWC56, of were isolated from watery kimchi and characterized. ΦWC53 belonged to Siphoviridae and ΦWC54 and ΦWC56 belonged to Myoviridae family. By one-step growth, the burst sizes were 5-260 particles/infected cells and the latent periods were 20-45 min. The phages infected spp., , and spp., differently by showing clear or turbid plaques. The phage adsorption rates on lactic acid bacteria were high on and low on and . However, the adsorption of ΦWC53 occurred variously among spp. and host grew well in the liquid culture without lysis after challenging by ΦWC53. Tolerances of these phages to temperature showed more various than those to pH. ΦWC53 was stable at 7 °C and 30 °C, but ΦWC54 and ΦWC56 were stable only at 7 °C. Therefore, three phages belonged to the different families and indicated diverse infection patterns on , and with various stabilities for pH and temperature.
PubMed: 34249390
DOI: 10.1007/s10068-021-00920-0 -
International Journal of Systematic and... Mar 2022The genera , , , and , which formed the family , have recently been merged within the family . Using genome sequences for 47 of the 52 named species from these genera,...
Phylogenomic and comparative genomic analyses of species: identification of molecular signatures specific for the genera , and and proposal for a novel genus gen. nov.
The genera , , , and , which formed the family , have recently been merged within the family . Using genome sequences for 47 of the 52 named species from these genera, we report here comprehensive phylogenomic and comparative analyses on protein sequences from these species using multiple approaches. In a phylogenomic tree based on concatenated sequences of 498 core proteins from these five genera, and in a 16S rRNA gene tree, members of the genera , and formed distinct strongly supported clades. In contrast, species grouped into two distinct unrelated clades designated as the ‘ main clade’ and ‘ clade 2’. The presence of these clades is also seen in a matrix of pairwise average amino acid identity based on core protein sequences. In parallel, comparative genomic studies on protein sequences from genomes have identified 46 conserved signature indels (CSIs) in diverse proteins that are unique characteristics of the different observed species clades. Of these identified CSIs, five, five and 13 CSIs are uniquely present in members of the genera , and , respectively. We also report here six and five CSIs that are exclusively present in the species from the main clade and clade 2, respectively, providing independent evidence supporting their distinctness from each other. The remaining 12 identified CSIs are commonly shared by some or all of the species from the genera , and , clarifying their interrelationships. The identified CSIs provide novel and reliable means for the identification/circumscription of members of the genera , and as well as the two species clades in molecular terms. Based on the strong phylogenetic and molecular evidence presented here, we propose that the genus be limited to only the species from the a main clade, whereas the species forming clade 2 should be transferred to a new genus gen. nov.
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Genomics; Leuconostoc; Leuconostocaceae; Oenococcus; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 35320068
DOI: 10.1099/ijsem.0.005284