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Microorganisms
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Food Microorganisms and Genomics
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Food Microorganisms and Genomics

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Food Microbiology".

Deadline for manuscript submissions: closed (15 July 2024) | Viewed by 19977

Special Issue Editors

Dr. Stefano Raimondi

E-Mail Website
Guest Editor
Department of Life Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
Interests: gut microbiota; probiotics; lactic acid bacteria; food microbiology; food biotechnology; prebiotics; microbiology; microbial biotechnology; environmental microbiology; microbial ecology; fermentation
Special Issues, Collections and Topics in MDPI journals
Dr. Alberto Amaretti

E-Mail Website
Guest Editor
Department of Life Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
Interests: Fermentation technologies; bioreactors; microbial biotechnology; probiotics; prebiotics; gut microbiota; food microbiology
Special Issues, Collections and Topics in MDPI journals
Dr. Francesco Candeliere

E-Mail Website
Co-Guest Editor
Department of Life Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
Interests: metagenomics; genomics; gut microbiota; probiotics; food microbiology; food biotechnology; microbial ecology; microbial biotechnology; environmental microbiology; fermentation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Metagenomics and whole-genome sequencing (WGS) revolutionized the study of complex microbial populations and drove the expansion of burst genomic analyses to an increasing number of taxonomic groups. In the last decade, the reduced costs and increased availability of next-generation sequencing techniques was also utilized in the study of food-related microorganisms, eliciting a holistic method to the study of microbiota, a genome-based approach for phylogeny, and a deeper exploration of the genic potential of technological microorganisms, probiotics, and foodborne pathogens.

This Special Issue of Microorganisms, entitled “Food Microorganisms and Genomics”, deals with studies based on NGS analyses for the description of microbial populations of foods, the monitoring of foodborne pathogens as well as probiotics and technological starters, and the genomic comparison of microbial taxa of food and nutraceutical interest. NGS-based studies on food–gut microbiota interactions are also included in the scope of this Special Issue.

Dr. Stefano Raimondi
Dr. Alberto Amaretti
Guest Editors

Dr. Francesco Candeliere
Co-Guest Editor

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Keywords

  • food microbiota
  • comparative genomics
  • foodborne pathogen
  • probiotics
  • technological starter

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Published Papers (12 papers)

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13 pages, 6971 KiB  
Article
Antimicrobial Resistance and Genomic Characterization of Campylobacter jejuni and Campylobacter coli Isolated from Retail Chickens in Beijing, China
by Yao Bai, Jiaqi Ma, Fengqin Li, Baowei Yang, Xiu Ren, Yeru Wang, Yujie Hu, Yinping Dong, Wei Wang, Jing Zhang, Shaofei Yan and Shenghui Cui
Microorganisms 2024, 12(8), 1601; https://doi.org/10.3390/microorganisms12081601 - 6 Aug 2024
Viewed by 780
Abstract
Objective Campylobacter species are the main causes of foodborne illness worldwide, posing significant threats to public health. This study aimed to investigate the antibiotic resistance and genomic characterization of C. jejuni/C.coli from retail chickens in Beijing. Methods Antimicrobial susceptibility testing was [...] Read more.
Objective Campylobacter species are the main causes of foodborne illness worldwide, posing significant threats to public health. This study aimed to investigate the antibiotic resistance and genomic characterization of C. jejuni/C.coli from retail chickens in Beijing. Methods Antimicrobial susceptibility testing was conducted on 126 C. jejuni/C. coli isolated from retail chickens in Beijing, following CLSI protocols. Whole genomes of all isolates were sequenced using the Illumina platform. Results More C. coli (83.82%) showed multi-drug resistance than C. jejuni (8.62%). Genomic analysis demonstrated 42 sequence types (STs) and 12 clonal complexes (CCs), from which CC828 and CC52 were dominant. cdtA, cdtB and cdtC encoding cytotoxic protein were present spontaneously in most C. jejuni but not found in any C. coli isolates. The abundances of antibiotic resistance genes (ARGs) and virulence genes (VGs) in C. jejuni and C. coli were significantly different, with ARGs numbered in C. coli and VGs in C. jejuni. Conclusions High prevalence of multi-drug resistance C. coli and C. jejuni isolated from Beijing chickens were challenging clinical antibiotic usages in the treatment of Campylobacter infection. The surveillance of particular C. jejuni and C. coli STs correlated with higher resistance and virulence needs to be strengthened in the future. Full article
(This article belongs to the Special Issue Food Microorganisms and Genomics)
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17 pages, 5544 KiB  
Article
The Metabolism of Leuconostoc Genus Decoded by Comparative Genomics
by Francesco Candeliere, Laura Sola, Enrico Busi, Maddalena Rossi, Alberto Amaretti and Stefano Raimondi
Microorganisms 2024, 12(7), 1487; https://doi.org/10.3390/microorganisms12071487 - 20 Jul 2024
Viewed by 978
Abstract
Leuconostoc encompasses a number of species that frequently appear in foods where they play different roles, ranging from ripening to spoiling. The number of available Leuconostoc genomes has recently increased and enabled the precise taxonomic and phylogenetic delineation of species. Nonetheless, a thorough [...] Read more.
Leuconostoc encompasses a number of species that frequently appear in foods where they play different roles, ranging from ripening to spoiling. The number of available Leuconostoc genomes has recently increased and enabled the precise taxonomic and phylogenetic delineation of species. Nonetheless, a thorough investigation of the functions and the metabolic potential of Leuconostoc species has never been accomplished. In this study, all the currently available 553 Leuconostoc genomes were downloaded from NCBI GenBank and annotated utilizing specific tools in order to reconstruct the metabolic potential of the genus in terms of carbohydrate hydrolysis and fermentative pathways, transporters, and anabolic potential. The analysis revealed that species cluster based on their metabolic potential, showing unique adaptation and ecological roles. Pentose phosphate and phosphoketolase pathways were highlighted as the main ones of central metabolism. The various identified PTS and ABC transporters showed adaptability to different sugars. The metabolic diversity described in this study not only supports the role of Leuconostoc spp. in natural ecosystems but also highlights their potential in industrial applications, particularly in the fermentation industry where their ability to metabolize a wide range of substrates can be harnessed for the production of various fermented foods and bioproducts. Full article
(This article belongs to the Special Issue Food Microorganisms and Genomics)
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13 pages, 2855 KiB  
Article
Comparative Gene Expression Analysis of Salmonella Typhimurium DT104 in Ground Chicken Extract and Brain Heart Infusion Broth
by Yanhong Liu, Fangyuan Zhang, Jabari L. Hawkins, Jake R. Elder, Gian Marco Baranzoni, Zuyi Huang, Pina M. Fratamico and Salina Parveen
Microorganisms 2024, 12(7), 1461; https://doi.org/10.3390/microorganisms12071461 - 18 Jul 2024
Viewed by 922
Abstract
Salmonella enterica Typhimurium DT104 (S. Typhimurium DT104) is an important foodborne pathogen that is associated with poultry and poultry products. Currently, there is very little information on the underlying molecular mechanisms that allow DT104 to survive and propagate in poultry meat and [...] Read more.
Salmonella enterica Typhimurium DT104 (S. Typhimurium DT104) is an important foodborne pathogen that is associated with poultry and poultry products. Currently, there is very little information on the underlying molecular mechanisms that allow DT104 to survive and propagate in poultry meat and the poultry processing environment. The current study assessed the global gene expression of DT104 in ground chicken extract (GCE) compared to brain heart infusion (BHI) medium using RNA-Seq technology. DT104 was grown to the early stationary phase (ESP), inoculated into GCE or BHI, and then re-grown to the log phase before RNA was extracted and transcripts were quantified by RNA-Seq. Gene expression for DT104 grown in GCE was then compared to that of DT104 grown in BHI for samples grown to the ESP. Growth in GCE resulted in the up-regulated expression of genes related to translation, carnitine metabolism (23–283-fold change), and cobalamin (vitamin B12) biosynthesis (14-fold change). In particular, the presence of carnitine in chicken meat, and thus, in GCE, which lacks carbohydrates, may allow Salmonella to utilize this compound as a carbon and nitrogen source. This study demonstrates that RNA-Seq data can provide a comprehensive analysis of DT104 gene expression in a food model for poultry products. This study also provides additional evidence for the importance of metabolic adaptation in the ability of S. enterica to successfully adapt to and occupy niches outside of its host and provides potential targets that could be used to develop intervention strategies to control Salmonella in poultry. Full article
(This article belongs to the Special Issue Food Microorganisms and Genomics)
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17 pages, 3878 KiB  
Article
Functional Analysis of Stress Resistance of Bacillus cereus SCL10 Strain Based on Whole-Genome Sequencing
by Yanzhen Mao, Ye Yang, Fu Lin, Hanyu Chu, Lijie Zhou, Jiaojiao Han, Jun Zhou and Xiurong Su
Microorganisms 2024, 12(6), 1168; https://doi.org/10.3390/microorganisms12061168 - 8 Jun 2024
Viewed by 974
Abstract
A Gram-positive, rod-shaped, aerobic, motile, and spore-forming bacterium, designated SCL10, was isolated from Acaudina molpadioides exposure to Co-60 radiation. In this study, whole-genome sequencing was performed to identify the strain as Bacillus cereus and functional characterization, with a focus on stress resistance. The [...] Read more.
A Gram-positive, rod-shaped, aerobic, motile, and spore-forming bacterium, designated SCL10, was isolated from Acaudina molpadioides exposure to Co-60 radiation. In this study, whole-genome sequencing was performed to identify the strain as Bacillus cereus and functional characterization, with a focus on stress resistance. The genome of the B. cereus SCL10 strain was sequenced and assembled, revealing a size of 4,979,182 bp and 5167 coding genes. The genes involved in biological functions were annotated by using the GO, COG, KEGG, NR, and Swiss-Prot databases. The results showed that genes related to alkyl hydroperoxide reductase (ahpC, ahpF), DNA-binding proteins from starved cells (dps), spore and biofilm formation (spoVG, spo0A, gerP), cold shock-like protein (cspC, cspE), ATP-dependent chaperone (clpB), and photolyase, small, acid-soluble spore protein (SASP) and DNA repair protein (recA, radD) could explain the stress resistance. These findings suggest that antioxidant activity, sporulation, biofilm formation, and DNA protection may be considered as the main resistance mechanisms under exposure to radiation in the B. cereus SCL10 strain. Full article
(This article belongs to the Special Issue Food Microorganisms and Genomics)
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20 pages, 7732 KiB  
Article
Comparative Genomics Reveals Genetic Diversity and Variation in Metabolic Traits in Fructilactobacillus sanfranciscensis Strains
by Xiaxia He, Yujuan Yu, Rober Kemperman, Luciana Jimenez, Faizan Ahmed Sadiq and Guohua Zhang
Microorganisms 2024, 12(5), 845; https://doi.org/10.3390/microorganisms12050845 - 23 Apr 2024
Cited by 1 | Viewed by 1497
Abstract
Fructilactobacillus sanfranciscensis is a significant and dominant bacterial species of sourdough microbiota from ecological and functional perspectives. Despite the remarkable prevalence of different strains of this species in sourdoughs worldwide, the drivers behind the genetic diversity of this species needed to be clarified. [...] Read more.
Fructilactobacillus sanfranciscensis is a significant and dominant bacterial species of sourdough microbiota from ecological and functional perspectives. Despite the remarkable prevalence of different strains of this species in sourdoughs worldwide, the drivers behind the genetic diversity of this species needed to be clarified. In this research, 14 F. sanfranciscensis strains were isolated from sourdough samples to evaluate the genetic diversity and variation in metabolic traits. These 14 and 31 other strains (obtained from the NCBI database) genomes were compared. The values for genome size and GC content, on average, turned out to 1.31 Mbp and 34.25%, respectively. In 45 F. sanfranciscensis strains, there were 162 core genes and 0 to 51 unique genes present in each strain. The primary functions of core genes were related to nucleotide, lipid transport, and amino acid, as well as carbohydrate metabolism. The size of core genes accounted for 41.18% of the pan-genome size in 14 F. sanfranciscensis strains, i.e., 0.70 Mbp of 1.70 Mbp. There were genetic variations among the 14 strains involved in carbohydrate utilization and antibiotic resistance. Moreover, exopolysaccharides biosynthesis-related genes were annotated, including epsABD, wxz, wzy. The Type IIA & IE CRISPR-Cas systems, pediocin PA-1 and Lacticin_3147_A1 bacteriocins operons were also discovered in F. sanfranciscensis. These findings can help to select desirable F. sanfranciscensis strains to develop standardized starter culture for sourdough fermentation, and expect to provide traditional fermented pasta with a higher quality and nutritional value for the consumers. Full article
(This article belongs to the Special Issue Food Microorganisms and Genomics)
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16 pages, 4165 KiB  
Article
Evaluation of Probiotic Properties and Safety of Lactobacillus helveticus LH10 Derived from Vinegar through Comprehensive Analysis of Genotype and Phenotype
by Yang Du, Jingru Xu, Jinquan Li and Renwei Wu
Microorganisms 2024, 12(4), 831; https://doi.org/10.3390/microorganisms12040831 - 19 Apr 2024
Cited by 2 | Viewed by 1561
Abstract
The probiotic potential of Lactobacillus helveticus LH10, derived from vinegar Pei, a brewing mixture, was assessed through genotype and phenotype analyses. The assembled genome was comprised of 1,810,276 bp and predicted a total of 2044 coding sequences (CDSs). Based on the whole genome [...] Read more.
The probiotic potential of Lactobacillus helveticus LH10, derived from vinegar Pei, a brewing mixture, was assessed through genotype and phenotype analyses. The assembled genome was comprised of 1,810,276 bp and predicted a total of 2044 coding sequences (CDSs). Based on the whole genome sequence analysis, two bacteriocin gene clusters were identified, while no pathogenic genes were detected. In in vitro experiments, L. helveticus LH10 exhibited excellent tolerance to simulated gastrointestinal fluid, a positive hydrophobic interaction with xylene, and good auto-aggregation properties. Additionally, this strain demonstrated varying degrees of resistance to five antibiotics, strong antagonistic activity against four tested pathogens, and no hemolytic activity. Therefore, L. helveticus LH10 holds great promise as a potential probiotic candidate deserving further investigation for its beneficial effects on human health. Full article
(This article belongs to the Special Issue Food Microorganisms and Genomics)
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17 pages, 5946 KiB  
Article
Cross-Phosphorylation between AgrC Histidine Kinase and the Noncognate Response Regulator Lmo1172 in Listeria monocytogenes under Benzalkonium Chloride Stress
by Tao Yu, Xiaojie Jiang, Xiaobo Xu, Ping Xu, Shuxing Qiu, Junlei Yin, David P. Hamilton and Xiaobing Jiang
Microorganisms 2024, 12(2), 392; https://doi.org/10.3390/microorganisms12020392 - 16 Feb 2024
Viewed by 1024
Abstract
Benzalkonium chloride (BC) is widely used for disinfection in the food industry. However, Listeria monocytogenes strains with resistance to BC have been reported recently. In L. monocytogenes, the Agr communication system consists of a membrane-bound peptidase AgrB, a precursor peptide AgrD, a [...] Read more.
Benzalkonium chloride (BC) is widely used for disinfection in the food industry. However, Listeria monocytogenes strains with resistance to BC have been reported recently. In L. monocytogenes, the Agr communication system consists of a membrane-bound peptidase AgrB, a precursor peptide AgrD, a histidine kinase (HK) AgrC, and a response regulator (RR) AgrA. Our previous study showed that the agr genes are significantly upregulated by BC adaptation. This study aimed to investigate the role of the Agr system in BC resistance in L. monocytogenes. Our results showed that the Agr system was involved in BC resistance. However, a direct interaction between BC and AgrC was not observed, nor between BC and AgrA. These results indicated that BC could induce the Agr system via an indirect action. Both AgrBD and AgrC were required for growth under BC stress. Nevertheless, when exposed to BC, the gene deletion mutant ∆agrA strain exhibited better growth performance than its parental strain. The RR Lmo1172 played a role in BC resistance in the ∆agrA strain, suggesting that Lmo1172 may be an alternative to AgrA in the phosphotransfer pathway. Phosphorylation of Lmo1172 by AgrC was observed in vitro. The cognate HK Lmo1173 of Lmo1172 was not involved in BC stress, regardless of whether it was as the wild-type or the ∆agrA mutant strain. Our evidence suggests that the HK AgrC cross-phosphorylates its noncognate RR Lmo1172 to cope with BC stress when the cognate RR AgrA is absent. In vivo, further studies will be required to detect phosphotransfer of AgrC/AgrA and AgrC/Lmo1172. Full article
(This article belongs to the Special Issue Food Microorganisms and Genomics)
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17 pages, 7468 KiB  
Article
Genome Analysis for Cholesterol-Lowing Action and Bacteriocin Production of Lactiplantibacillus plantarum WLPL21 and ZDY04 from Traditional Chinese Fermented Foods
by Kui Zhao, Liang Qiu, Xueying Tao, Zhihong Zhang and Hua Wei
Microorganisms 2024, 12(1), 181; https://doi.org/10.3390/microorganisms12010181 - 17 Jan 2024
Cited by 1 | Viewed by 1505
Abstract
Lactiplantibacillus plantarum, a typical ecological species against pathogens, used due to its bacteriocin yield in fermented foods, was proven to have the capacity to lower cholesterol. In this study, using L. plantarum ATCC8014 as the control, L. plantarum WLPL21 and ZDY04 were [...] Read more.
Lactiplantibacillus plantarum, a typical ecological species against pathogens, used due to its bacteriocin yield in fermented foods, was proven to have the capacity to lower cholesterol. In this study, using L. plantarum ATCC8014 as the control, L. plantarum WLPL21 and ZDY04 were probed with whole-genome sequencing to ascertain their potential ability to lower cholesterol and yield bacteriocins, as well as to further evaluate their survival capacity in vitro. Our results showed 386 transport-system genes in both L. plantarum WLPL21 and ZDY04. Correspondingly, the in vitro results showed that L. plantarum WLPL21 and ZDY04 could remove cholesterol at 49.23% and 41.97%, respectively, which is 1.89 and 1.61 times that of L. plantarum ATCC8014. The survival rates of L. plantarum WLPL21 and ZDY04 in 1% H2O2, pH 3.0, and 0.3% bile salt were higher than those of L. plantarum ATCC8014. Our results exhibited a complete gene cluster for bacteriocin production encoded by L. plantarum WLPL21 and ZDY04, including plnJKR, plnPQAB, plnEFI, plnSUVWY, and plnJK; and plnMN, plnPQA and plnEFI, respectively, compared with only plnEF in L. plantarum ATCC8014. The present study suggests that the combination of genomic analysis with in vitro evaluations might be useful for exploring the potential functions of probiotics. Full article
(This article belongs to the Special Issue Food Microorganisms and Genomics)
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19 pages, 3197 KiB  
Article
Dissecting the Genetic Basis of the Technological, Functional, and Safety Characteristics of Lacticaseibacillus paracasei SRX10
by Christina S. Kamarinou, Despoina E. Kiousi, Panagiotis Repanas, Anthoula A. Argyri, Nikos G. Chorianopoulos and Alex Galanis
Microorganisms 2024, 12(1), 93; https://doi.org/10.3390/microorganisms12010093 - 2 Jan 2024
Viewed by 2180
Abstract
Nonstarter lactic acid bacteria (NSLAB) are major contributors to the unique characteristics (e.g., aroma, flavor, texture) of dairy and nondairy fermented products. Lc. paracasei SRX10 is an NSLAB strain originally isolated from a traditional Greek cheese and previously shown to exhibit favorable biotechnological [...] Read more.
Nonstarter lactic acid bacteria (NSLAB) are major contributors to the unique characteristics (e.g., aroma, flavor, texture) of dairy and nondairy fermented products. Lc. paracasei SRX10 is an NSLAB strain originally isolated from a traditional Greek cheese and previously shown to exhibit favorable biotechnological characteristics. More specifically, the strain showed tolerance to simulated gastrointestinal conditions, exopolysaccharide (EPS) biosynthetic capacity, and lack of hemolytic activity and was used in the production of yoghurt and feta cheese with distinct organoleptic characteristics. The aim of the present study was to investigate these traits at the genome level through whole-genome sequencing (WGS), annotation, and comparative genomics. Functional annotation of the genome revealed that Lc. paracasei SRX10 can utilize different carbon sources, leading to the generation of flavor compounds, including lactic acid, acetate, ethanol, and acetoin. Similarly, full clusters for fatty acid biosynthesis, protein and peptide degradation, as well as genes related to survival under extreme temperatures, osmotic shock, and oxidative stress were annotated. Importantly, no transferable antibiotic resistance genes or virulence factors were identified. Finally, strain-specific primers based on genome-wide polymorphisms were designed for the efficient and rapid identification of Lc. paracasei SRX10 via multiplex PCR in fermented products. Full article
(This article belongs to the Special Issue Food Microorganisms and Genomics)
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15 pages, 1175 KiB  
Article
Genetic and Phenotypic Virulence Potential of Non-O1/Non-O139 Vibrio cholerae Isolated from German Retail Seafood
by Quantao Zhang, Thomas Alter, Eckhard Strauch, Jens Andre Hammerl, Keike Schwartz, Maria Borowiak, Carlus Deneke and Susanne Fleischmann
Microorganisms 2023, 11(11), 2751; https://doi.org/10.3390/microorganisms11112751 - 11 Nov 2023
Cited by 2 | Viewed by 1672
Abstract
Non-O1 and non-O139 Vibrio cholerae (NOVC) can cause gastrointestinal infections in humans. Contaminated food, especially seafood, is an important source of human infections. In this study, the virulence potential of 63 NOVC strains isolated from retail seafood were characterized at the genotypic and [...] Read more.
Non-O1 and non-O139 Vibrio cholerae (NOVC) can cause gastrointestinal infections in humans. Contaminated food, especially seafood, is an important source of human infections. In this study, the virulence potential of 63 NOVC strains isolated from retail seafood were characterized at the genotypic and phenotypic levels. Although no strain encoded the cholera toxin (CTX) and the toxin-coregulated pilus (TCP), several virulence factors, including the HlyA hemolysin, the cholix toxin ChxA, the heat-stable enterotoxin Stn, and genes coding for the type 3 and type 6 secretion systems, were detected. All strains showed hemolytic activity against human and sheep erythrocytes: 90% (n = 57) formed a strong biofilm, 52% (n = 33) were highly motile at 37 °C, and only 8% (n = 5) and 14% (n = 9) could resist ≥60% and ≥40% human serum, respectively. Biofilm formation and toxin regulation genes were also detected. cgMLST analysis demonstrated that NOVC strains from seafood cluster with clinical NOVC strains. Antimicrobial susceptibility testing (AST) results in the identification of five strains that developed non-wildtype phenotypes (medium and resistant) against the substances of the classes of beta-lactams (including penicillin, carbapenem, and cephalosporin), polymyxins, and sulphonamides. The phenotypic resistance pattern could be partially attributed to the acquired resistance determinants identified via in silico analysis. Our results showed differences in the virulence potential of the analyzed NOVC isolated from retail seafood products, which may be considered for further pathogenicity evaluation and the risk assessment of NOVC isolates in future seafood monitoring. Full article
(This article belongs to the Special Issue Food Microorganisms and Genomics)
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23 pages, 5838 KiB  
Article
Characterization of Microbial Diversity of Two Tomato Cultivars through Targeted Next-Generation Sequencing 16S rRNA and ITS Techniques
by Rukayat Abiola Abdulsalam, Oluwatosin Ademola Ijabadeniyi, Errol D. Cason and Saheed Sabiu
Microorganisms 2023, 11(9), 2337; https://doi.org/10.3390/microorganisms11092337 - 18 Sep 2023
Cited by 1 | Viewed by 1828
Abstract
Even though the nutritional and economic values of Solanum lycopersicum (tomato) are substantially impacted by microbial spoilage, the available data on its microbial community, particularly during spoilage, are limited and have primarily been characterized using conventional culture-dependent methods. This study employed a targeted [...] Read more.
Even though the nutritional and economic values of Solanum lycopersicum (tomato) are substantially impacted by microbial spoilage, the available data on its microbial community, particularly during spoilage, are limited and have primarily been characterized using conventional culture-dependent methods. This study employed a targeted high-throughput next-generation sequencing method to longitudinally characterize the microbial diversity of two South African tomato cultivars (jam and round) at varied storage intervals (1, 6, and 12 days). Throughout the storage period, the bacterial communities of the two cultivars were more diverse than the fungal communities. The microbial diversity of both bacteria and fungi was greater and comparable between the cultivars on day 1, but becomes distinct as the storage period increases, with round tomatoes being more diverse than jam tomato, though, on day 12, jam tomato develops greater diversity than round tomato. Overall, the most abundant phyla (though Proteobacteria was most dominant) were Proteobacteria, Firmicutes, and Bacteriodota in the bacterial communities, while Ascomycota and Basidiomycota formed most fungal communities with Ascomycota being dominant. At the genus level, Pantoea and Klebsiella (bacteria), Hanseniaspora, Stemphylium, and Alternaria (fungi) were prevalent. Taken together, this study casts light on a broad microbial diversity profile thus, confirms the cultivars’ diversity and abundance differences. Full article
(This article belongs to the Special Issue Food Microorganisms and Genomics)
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15 pages, 1972 KiB  
Article
Whole-Genome Sequence of Lactococcus lactis Subsp. lactis LL16 Confirms Safety, Probiotic Potential, and Reveals Functional Traits
by Justina Mileriene, Jurgita Aksomaitiene, Kristina Kondrotiene, Tora Asledottir, Gerd Elisabeth Vegarud, Loreta Serniene and Mindaugas Malakauskas
Microorganisms 2023, 11(4), 1034; https://doi.org/10.3390/microorganisms11041034 - 15 Apr 2023
Cited by 15 | Viewed by 3294
Abstract
Safety is the most important criteria of any substance or microorganism applied in the food industry. The whole-genome sequencing (WGS) of an indigenous dairy isolate LL16 confirmed it to be Lactococcus lactis subsp. lactis with genome size 2,589,406 bp, 35.4% GC content, 246 [...] Read more.
Safety is the most important criteria of any substance or microorganism applied in the food industry. The whole-genome sequencing (WGS) of an indigenous dairy isolate LL16 confirmed it to be Lactococcus lactis subsp. lactis with genome size 2,589,406 bp, 35.4% GC content, 246 subsystems, and 1 plasmid (repUS4). The Nextera XT library preparation kit was used to generate the DNA libraries, and the sequencing was carried out on an Illumina MiSeq platform. In silico analysis of L. lactis LL16 strain revealed non-pathogenicity and the absence of genes involved in transferable antimicrobial resistances, virulence, and formation of biogenic amines. One region in the L. lactis LL16 genome was identified as type III polyketide synthases (T3PKS) to produce putative bacteriocins lactococcin B, and enterolysin A. The probiotic and functional potential of L. lactis LL16 was investigated by the presence of genes involved in adhesion and colonization of the host’s intestines and tolerance to acid and bile, production of enzymes, amino acids, and B-group vitamins. Genes encoding the production of neurotransmitters serotonin and gamma-aminobutyric acid (GABA) were detected; however, L. lactis LL16 was able to produce only GABA during milk fermentation. These findings demonstrate a variety of positive features that support the use of L. lactis LL16 in the dairy sector as a functional strain with probiotic and GABA-producing properties. Full article
(This article belongs to the Special Issue Food Microorganisms and Genomics)
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