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Wigmore SM, Nankervis SA, Watson L, Bean DC. Staphylococcal carriage among captive dingoes (Canis dingo) in Victoria, Australia. Vet Microbiol 2024; 294:110104. [PMID: 38768556 DOI: 10.1016/j.vetmic.2024.110104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 05/22/2024]
Abstract
The evolutionary lineage and taxonomy of the Australian dingo is controversial, however recent genomic and gut metagenomic research has suggested that dingoes are evolutionarily distinct from modern dogs. Staphylococcus species are known commensal organisms of dogs and other mammals. In this study we took the opportunity to determine the carriage rate and antimicrobial resistance profiles of Staphylococcus species from 15 captive Australian dingoes. S. pseudintermedius was the only coagulase-positive species recovered, isolated from 6/15 (40%) and 9/13 (69%) of the animals during the 2020 (winter) and 2021 (summer) sampling times, respectively. Twenty-three coagulase-negative isolates were characterised, with S. equorum being the most frequently (20/23, 87%) recovered species. Two isolates of S. equorum had their genomes sequenced to learn more about this species. Antimicrobial resistance amongst both coagulase-positive and -negative isolates was low; with resistance to only 3 of 12 antimicrobials observed: penicillin, erythromycin, and trimethoprim. We have shown that the Australian dingo is a host organism for S. pseudintermedius much like it is in dogs, however the carriage rate was lower than has previously been reported from dogs in Australia.
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Affiliation(s)
- Sarah M Wigmore
- Microbiology Research Group, Institute of Innovation, Science and Sustainability, Federation University Australia, PO Box 663, Ballarat, Victoria 3353, Australia
| | - Scott A Nankervis
- Microbiology Research Group, Institute of Innovation, Science and Sustainability, Federation University Australia, PO Box 663, Ballarat, Victoria 3353, Australia
| | - Lynette Watson
- Dingo Discovery Sanctuary and Research Centre, PO Box 502, Gisborne, Victoria 3437, Australia
| | - David C Bean
- Microbiology Research Group, Institute of Innovation, Science and Sustainability, Federation University Australia, PO Box 663, Ballarat, Victoria 3353, Australia.
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2
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Lee H, Cho H, Lim Y, Park S, Lee J. Safety, quality, and microbial community analysis of salt-fermented shrimp ( Saeu-jeot) in South Korea. Heliyon 2024; 10:e26006. [PMID: 38390104 PMCID: PMC10881329 DOI: 10.1016/j.heliyon.2024.e26006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
This study thoroughly explores the quality and safety aspects of saeu-jeot, a popular salt-fermented shrimp in South Korea, with a specific focus on products fermented in underground tunnels. In this study, an extensive analysis of key quality factors (pH, salinity, total nitrogen [TN], and amino nitrogen [AN]), along with detailed investigation into chemical hazards (volatile basic nitrogen [VBN] and biogenic amines [BAs]), and microbiological hazards (total aerobic bacteria [TAB], fecal indicator bacteria, halophilic bacteria, and foodborne pathogens) were performed. The results indicate that the shrimp grade did not dramatically affect the quality and safety of the saeu-jeot. However, given the prevalent small-scale production of saeu-jeot, the study strongly underscores the pressing need for the establishment of a standardized manufacturing process. The absence of grade-dependent variations in quality highlights the critical importance of implementing standardized procedures to ensure the consistent quality and safety of saeu-jeot, particularly in the context of its frequent small-scale production. These findings provide crucial insights for the industry to enhance practices and meet quality and safety standards effectively.
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Affiliation(s)
- Heeyoung Lee
- Food Standard Research Center, Korea Food Research Institute, Jeollabuk-do 55365, Republic of Korea
| | - Hyunjin Cho
- Department of Food & Nutrition, Dong-eui University, Busan 47340, Republic of Korea
| | - Yeongsil Lim
- Department of Food & Nutrition, Dong-eui University, Busan 47340, Republic of Korea
| | - Sunhyun Park
- Food Standard Research Center, Korea Food Research Institute, Jeollabuk-do 55365, Republic of Korea
- Department of Food Science and Technology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jeeyeon Lee
- Department of Food & Nutrition, Dong-eui University, Busan 47340, Republic of Korea
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3
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Busetta G, Garofalo G, Claps S, Sardina MT, Franciosi E, Alfonzo A, Francesca N, Moschetti G, Settanni L, Gaglio R. The wooden shelf surface and cheese rind mutually exchange microbiota during the traditional ripening process. Int J Food Microbiol 2024; 409:110478. [PMID: 37948980 DOI: 10.1016/j.ijfoodmicro.2023.110478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/24/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
The rind acts as a protective barrier for internally-bacterial ripened cheeses. Unlike surface-inoculated smear cheeses, centripetal maturation is not assumed to occur in these cheeses. This research was aimed to evaluate the microbial diversity of the wooden shelves used for the ripening of Protected Denomination of Origin (PDO) Pecorino di Filiano and Protected Geographical Indication (PGI) Canestrato di Moliterno cheeses. The microorganisms associated with the rind of these cheeses were also investigated. Both wooden shelf surfaces and cheese rinds were sampled by brushing method to collect their biofilms. Wooden shelves showed levels of total mesophilic microorganisms (TMM) between 5.6 and 7.2 log CFU/cm2, while cheese rinds between 6.1 and 7.8 log CFU/cm2. The major dairy pathogens (Salmonella spp., Listeria monocytogenes, Escherichia coli, and Staphylococcus aureus) were never detected, while mesophilic and thermophilic bacteria dominated the surfaces of all wooden shelves and cheese rinds. LAB community was represented by Enterococcus spp., Leuconostoc spp., and Marinilactibacillus spp. Among yeasts, Debaryomyces spp., Candida spp., were identified, while Aspergillus spp., and Penicillium spp., dominated the community of filamentous fungi. MiSeq Illumina analysis identified 15 phyla, 13 classes, 28 orders, 54 families, and 56 genera among bacteria. Staphylococcus spp. was identified from all wooden surfaces, with a maximum abundance of 71 %. Brevibacterium, Corynebacterium and halophilic bacteria were detected in almost all samples. Regarding fungi, wooden shelves mainly hosted Aspergillus, Penicillium and Debaryomyces hansenii, while cheese rinds especially Penicillium and D. hansenii. Alpha diversity confirmed a strict correlation between the microbiota of wooden shelves and that of cheese rinds for the majority of factories. This study confirmed that the wooden shelves used for cheese ripening are microbiologically active and represent safe systems. Furthermore, the results of this work clarified the transfer flow between wooden shelves and PDO Pecorino di Filiano and PGI Canestrato di Moliterno cheese surfaces: smear-active microorganisms are mainly transferred from wooden shelves to cheese rind, which potentially contribute to the development of the final organoleptic characteristics; meanwhile, cheeses transfer LAB that are potentially involved in defining the safety aspects of the shelves.
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Affiliation(s)
- Gabriele Busetta
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Viale delle Scienze 4, 90128 Palermo, Italy
| | - Giuliana Garofalo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Viale delle Scienze 4, 90128 Palermo, Italy
| | - Salvatore Claps
- CREA Research, Centre for Animal Production and Aquaculture, S.S. 7 Via Appia, Bella Muro, PZ 85051, Italy
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Viale delle Scienze 4, 90128 Palermo, Italy
| | - Elena Franciosi
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Antonio Alfonzo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Viale delle Scienze 4, 90128 Palermo, Italy
| | - Nicola Francesca
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Viale delle Scienze 4, 90128 Palermo, Italy
| | - Giancarlo Moschetti
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Viale delle Scienze 4, 90128 Palermo, Italy
| | - Luca Settanni
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Viale delle Scienze 4, 90128 Palermo, Italy.
| | - Raimondo Gaglio
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Viale delle Scienze 4, 90128 Palermo, Italy
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4
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Ye R, Tomo C, Chan N, Wolfe BE. Penicillium molds impact the transcriptome and evolution of the cheese bacterium Staphylococcus equorum. mSphere 2023; 8:e0004723. [PMID: 37219436 PMCID: PMC10449494 DOI: 10.1128/msphere.00047-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/17/2023] [Indexed: 05/24/2023] Open
Abstract
The observation that Penicillium molds can inhibit the growth of Staphylococcus was a catalyst for the antibiotic revolution. Considerable attention has been paid to purified Penicillium metabolites that inhibit bacteria, but little is known about how Penicillium species impact the ecology and evolution of bacteria in multispecies microbial communities. Here, we investigated how four different species of Penicillium can impact global transcription and evolution of a widespread Staphylococcus species (S. equorum) using the cheese rind model microbiome. Through RNA sequencing, we identified a core transcriptional response of S. equorum against all five tested Penicillium strains, including upregulation of thiamine biosynthesis, fatty acid degradation, and amino acid metabolism as well as downregulation of genes involved in the transport of siderophores. In a 12-week evolution experiment where we co-cultured S. equorum with the same Penicillium strains, we observed surprisingly few non-synonymous mutations across S. equorum populations evolved with the Penicillium species. A mutation in a putative DHH family phosphoesterase gene only occurred in populations evolved without Penicillium and decreased the fitness of S. equorum when co-cultured with an antagonistic Penicillium strain. Our results highlight the potential for conserved mechanisms of Staphylococcus-Penicillium interactions and demonstrate how fungal biotic environments may constrain the evolution of bacterial species.IMPORTANCEFungi and bacteria are commonly found co-occurring both in natural and synthetic microbiomes, but our understanding of fungal-bacterial interactions is limited to a handful of species. Conserved mechanisms of interactions and evolutionary consequences of fungal-bacterial interactions are largely unknown. Our RNA sequencing and experimental evolution data with Penicillium species and the bacterium S. equorum demonstrate that divergent fungal species can elicit conserved transcriptional and genomic responses in co-occurring bacteria. Penicillium molds are integral to the discovery of novel antibiotics and production of certain foods. By understanding how Penicillium species affect bacteria, our work can further efforts to design and manage Penicillium-dominated microbial communities in industry and food production.
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Affiliation(s)
- Ruby Ye
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Christopher Tomo
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Neal Chan
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Benjamin E. Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, USA
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5
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Vázquez L, Srednik ME, Rodríguez J, Flórez AB, Mayo B. Antibiotic Resistance/Susceptibility Profiles of Staphylococcus equorum Strains from Cheese, and Genome Analysis for Antibiotic Resistance Genes. Int J Mol Sci 2023; 24:11657. [PMID: 37511416 PMCID: PMC10380560 DOI: 10.3390/ijms241411657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
In food, bacteria carrying antibiotic resistance genes could play a prominent role in the spread of resistance. Staphylococcus equorum populations can become large in a number of fermented foods, yet the antibiotic resistance properties of this species have been little studied. In this work, the resistance/susceptibility (R/S) profile of S. equorum strains (n = 30) from cheese to 16 antibiotics was determined by broth microdilution. The minimum inhibitory concentration (MIC) for all antibiotics was low in most strains, although higher MICs compatible with acquired genes were also noted. Genome analysis of 13 strains showed the S. equorum resistome to be composed of intrinsic mechanisms, acquired mutations, and acquired genes. As such, a plasmidic cat gene providing resistance to chloramphenicol was found in one strain; this was able to provide resistance to Staphylococcus aureus after electroporation. An msr(A) polymorphic gene was identified in five strains. The Mrs(A) variants were associated with variable resistance to erythromycin. However, the genetic data did not always correlate with the phenotype. As such, all strains harbored a polymorphic fosB/fosD gene, although only one acquired copy was associated with strong resistance to fosfomycin. Similarly, a plasmid-associated blaR1-blaZI operon encoding a penicillinase system was identified in five ampicillin- and penicillin G-susceptible strains. Identified genes not associated with phenotypic resistance further included mph(C) in two strains and norA in all strains. The antibiotic R/S status and gene content of S. equorum strains intended to be employed in food systems should be carefully determined.
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Affiliation(s)
- Lucía Vázquez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
| | - Mariela E Srednik
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Javier Rodríguez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
| | - Ana Belén Flórez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
| | - Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
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6
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Chen Y, Liu X, Li Q, Cai X, Wu W, Wu Q, Yuan W, Deng X, Liu Z, Zhao S, Wang B. Integrated genomics and transcriptomics reveal the extreme heavy metal tolerance and adsorption potentiality of Staphylococcus equorum. Int J Biol Macromol 2023; 229:388-400. [PMID: 36592848 DOI: 10.1016/j.ijbiomac.2022.12.298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/05/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022]
Abstract
In this study, we successfully isolated 11 species of cadmium-tolerant bacterium from Pu-erh rhizosphere soil, of which Staphylococcus equorum PU1 showed the highest cadmium tolerance, with a minimum inhibitory concentration (MIC) value of 500 mg/L. The cadmium removal efficiency of PU1 in 400 mg/L cadmium medium reached 58.7 %. Based on the Nanopore PromethION and Illumina NovaSeq platforms, we successfully obtained the complete PU1 genome with a size of 2,705,540 bp, which encoded 2729 genes. We further detected 82 and 44 indel mutations in the PU1 genome compared with the KS1039 and KM1031 genomes from the database. Transcriptional analysis showed that the expression of 11 genes in PU1 increased with increasing cadmium concentrations (from 0 to 200, then to 400 mg/L), which encoded cadmium resistance, cadmium transport, and mercury resistance genes. In addition, some genes showed differential expression patterns with changes in cadmium concentration, including quinone oxidoreductase-like protein, ferrous iron transport protein, and flavohemoprotein. Gene Ontology (GO) functions, including oxidation reduction process and oxidoreductase activity functions, and KEGG pathways, including glycolysis/gluconeogenesis and biosynthesis of secondary metals, were also considered closely related to the extreme cadmium tolerance of PU1. This study provides novel insight into the cadmium tolerance mechanism of bacteria.
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Affiliation(s)
- Yaping Chen
- College of Tea Science, Yunnan Agricultural University, Kunming, China; College of Plant Protection, Yunnan Agricultural University, Kunming, China; Yunnan Organic Tea Industry Intelligent Engineering Research Center, Kunming, China
| | - Xiaohui Liu
- College of Tea Science, Yunnan Agricultural University, Kunming, China
| | - Qiang Li
- College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Xiaobo Cai
- Yunnan Organic Tea Industry Intelligent Engineering Research Center, Kunming, China; College of Big Data, Yunnan Agricultural University, Kunming, China; Key Laboratory of Intelligent Organic Tea Garden Construction in Universities of Yunnan Province, Kunming, China
| | - Wendou Wu
- Yunnan Organic Tea Industry Intelligent Engineering Research Center, Kunming, China; College of Big Data, Yunnan Agricultural University, Kunming, China; Key Laboratory of Intelligent Organic Tea Garden Construction in Universities of Yunnan Province, Kunming, China
| | - Qi Wu
- College of Science, Yunnan Agricultural University, Kunming, China
| | - Wenxia Yuan
- College of Tea Science, Yunnan Agricultural University, Kunming, China
| | - Xiujuan Deng
- College of Tea Science, Yunnan Agricultural University, Kunming, China
| | - Zhiwe Liu
- College of Tea Science, Yunnan Agricultural University, Kunming, China
| | - Shengnan Zhao
- College of Tea Science, Yunnan Agricultural University, Kunming, China
| | - Baijuan Wang
- College of Tea Science, Yunnan Agricultural University, Kunming, China; College of Big Data, Yunnan Agricultural University, Kunming, China; Key Laboratory of Intelligent Organic Tea Garden Construction in Universities of Yunnan Province, Kunming, China.
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Van der Veken D, Leroy F. Prospects for the applicability of coagulase-negative cocci in fermented-meat products using omics approaches. Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Chen J, Zhang J, Yang Z, Niu Y, Cai Z, Wang J, Yin L, Lin Y, Lu X. Characterization of indigenous coagulase-negative staphylococci isolated from Chinese spontaneously fermented meat products. Microbiol Res 2022; 263:127160. [PMID: 35944356 DOI: 10.1016/j.micres.2022.127160] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/03/2022] [Accepted: 08/03/2022] [Indexed: 10/16/2022]
Abstract
Technological, safety-related and volatile properties were analyzed in coagulase-negative staphylococci (CNS) isolates from Chinese spontaneously fermented meat products. A total of 107 CNS isolates were identified via 16 S rRNA sequencing, and the most recovered species were S. saprophyticus (53.3 %), S. edaphicus (12.1 %), and S. epidermidis (10.3 %). Among them, 58 CNS isolates belonging to 9 species were selected with higher activities of catalase, nitrate reductase, proteolysis, and lipolysis, as well as higher tolerance to stressful environmental conditions. Then, 7 CNS isolates belonging to 4 species were further selected based upon excellent technological characteristics, lack of hemolysis and antibiotic resistance, and a low production of biogenic amines. The volatile profiles of these 7 strains cultivated in pork broth was determined. S. casei No. 1 produced significant amounts of phenethyl alcohol, geraniol, and 3-methyl-butanol. S. xylosus No. 120 produced the highest amount of methyl ketones with the potential to provide dry-cured odor of fermented meats. The volatile profile was highly strain dependent. Several CNS identified in this study have the potential to be used as the starter cultures for fermented meat products.
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Affiliation(s)
- Juan Chen
- College of Food Science and Technology, Southwest Minzu University, Chengdu, China; Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
| | - Jingbin Zhang
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
| | - Ziyao Yang
- College of Food Science and Technology, Southwest Minzu University, Chengdu, China
| | - Ying Niu
- College of Food Science and Technology, Southwest Minzu University, Chengdu, China
| | - Zijian Cai
- College of Food Science and Technology, Southwest Minzu University, Chengdu, China
| | - Jie Wang
- College of Food Science and Technology, Southwest Minzu University, Chengdu, China
| | - Liguo Yin
- Solid-state Fermentation Resource Utilization Key Laboratory of Sichuan Province, Yibin University, Yibin, China
| | - Yaqiu Lin
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China.
| | - Xiaonan Lu
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada.
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Heo S, Kim T, Na HE, Lee G, Lee JH, Jeong DW. Transcriptomic analysis of Staphylococcus equorum KM1031 from the high-salt fermented seafood jeotgal under chloramphenicol, erythromycin and lincomycin stresses. Sci Rep 2022; 12:15541. [PMID: 36109627 PMCID: PMC9477809 DOI: 10.1038/s41598-022-19897-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
Staphylococcus equorum strain KM1031 is resistant to chloramphenicol, erythromycin and lincomycin. To shed light on the genetic factors underlying these antibiotic resistances, we determined the global gene expression profile of S. equorum KM1031 using RNA sequencing. During chloramphenicol, erythromycin and lincomycin treatment, 8.3% (183/2,336), 16.0% (354/2,336), and 2.9% (63/2,336) of S. equorum KM1031 genes exhibited significant differences in expression, respectively. These three antibiotics upregulated genes related to efflux and downregulated genes related to transporters. Antibiotic treatment also upregulated osmoprotectant-related genes involved in salt tolerance. To identify specific genes functionally related to antibiotic resistance, we compared the genome of strain KM1031 with those of three S. equorum strains that are sensitive to these three antibiotics. We identified three genes of particular interest: an antibiotic biosynthesis monooxygenase gene (abm, AWC34_RS01805) related to chloramphenicol resistance, an antibiotic ABC transporter ATP-binding protein gene (msr, AWC34_RS11115) related to erythromycin resistance, and a lincosamide nucleotydyltransferase gene (lnuA, AWC34_RS13300) related to lincomycin resistance. These genes were upregulated in response to the corresponding antibiotic; in particular, msr was upregulated more than fourfold by erythromycin treatment. Finally, the results of RNA sequencing were validated by quantitative real-time PCR. This transcriptomic analysis provides genetic evidence regarding antibiotic stress responses of S. equorum strain KM1031.
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10
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Chiou WC, Lai WH, Cai YL, Du ML, Lai HM, Chen JC, Huang HC, Liu HK, Huang C. Gut microbiota-directed intervention with high-amylose maize ameliorates metabolic dysfunction in diet-induced obese mice. Food Funct 2022; 13:9481-9495. [PMID: 35993118 DOI: 10.1039/d2fo01211a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Obesity is a chronic disease that may lead to the development of metabolic diseases, cardiovascular diseases, and cancers and has been predicted to affect one billion adults by 2030. Owing to the pivotal role of the gut microbiota in health, including metabolism and energy homeostasis, dietary fiber, the primary energy resource for the gut microbiota, not only helps reduce appetite and short-term food intake but also modulates the structure of the gut microbiota. In this study, we investigated whether high-amylose maize (HAM), with a particular amount of dietary fiber, improves dysmetabolism and gut microbiota dysbiosis in diet-induced obese mice. Promisingly, the HAM dietary intervention not only reduced body weight gain, adipocyte hypertrophy, and dyslipidemia but also mitigated non-alcoholic fatty liver disease, insulin resistance, impaired glucose tolerance, and inflammation in the liver and epididymal white adipose tissues in high-fat diet (HFD)-fed obese mice. In addition, the HAM dietary intervention ameliorated gut microbiota dysbiosis in HFD-fed mice. Changes in families, genera, and species of gut biota that have a relative abundance of 0.01% in at least one group were scrutinized. At the species level, HAM dietary intervention increased Bifidobacterium pseudolongum, Bifidobacterium animalis, Bifidobacterium bifidum, and Lactobacillus paraplantarum and decreased Streptococcus agalactiae, Mucispirillum schaedleri, and Alistipes indistinctus. This change in the gut microbiota driven by the HAM diet was strongly associated with obesity-related indices, highlighting the nutraceutical potential of HAM for improving overall metabolic health. Taken together, this study demonstrates the potential of the HAM diet for mediating metabolic syndrome and gut microbiota dysbiosis.
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Affiliation(s)
- Wei-Chung Chiou
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - Wei-Han Lai
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - Yu-Lin Cai
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - Meng-Lun Du
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Hsi-Mei Lai
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Jui-Chieh Chen
- Department of Biochemical Science and Technology, National Chiayi University, Chiayi, Taiwan
| | - Hsiu-Chen Huang
- Department of Applied Science, National Tsing Hua University South Campus, Hsinchu, Taiwan.,Center for Teacher Education, National Tsing Hua University, Hsinchu, Taiwan
| | - Hui-Kang Liu
- Division of Basic Chinese Medicine, National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei, Taiwan.,PhD Program for the Clinical Drug Discovery from Herbal Medicine, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Cheng Huang
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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11
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Transcriptomic Analysis of Staphylococcus equorum KM1031, Isolated from the High-Salt Fermented Seafood Jeotgal, under Salt Stress. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8080403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Staphylococcus equorum is a potential starter for Korean high-salt fermented foods because of its salt tolerance and enzymatic activities that contribute to enhanced sensory properties of the food products. However, the mechanisms of salt tolerance of S. equorum are not fully understood. Here, RNA sequencing was performed on S. equorum strain KM1031 exposed to 7% NaCl (w/v) for 2 and 4 h to determine global gene expression changes. Salt pressure for 2 and 4 h resulted in significant differential expression of 4.8% (106/2209) and 6.1% (134/2209) of S. equorum KM1031 genes, respectively. Twenty-five core genes were differentially expressed on salt treatment for both 2 and 4 h, seven of which were related to osmoprotectant uptake and synthesis. We analyzed the genome of strain KM1031 and identified osmoprotectant uptake (Opu) systems, potassium importers, sodium exporters, and the glycine betaine synthesis system. The RNA sequencing results indicated that the OpuD system and glycine betaine synthesis might play the main roles in the salt tolerance of strain KM1031. Finally, the results of RNA sequencing were validated by quantitative real-time PCR of likely salt stress-related genes. This transcriptomic analysis provides evidence regarding the osmotic stress responses of S. equorum strain KM1031.
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Fruit Microbial Communities of the Bisucciu Sardinian Apricot Cultivar (Prunus armeniaca L.) as a Reservoir of New Brewing Starter Strains. FERMENTATION 2022. [DOI: 10.3390/fermentation8080364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Local fruit cultivars may improve the originality of specialty beers both directly, by conferring peculiar tastes and flavors, and indirectly, as a reservoir of new starter strains. Accordingly, the fungal and bacterial communities of Bisucciu fruit, a Sardinian apricot cultivar used to produce a local fruit beer, were here investigated by culture-dependent methods. From the 16S rDNA and ITS sequence analyses of 68 epiphytic isolates, 5 bacterial species and 19 fungal species were identified. Aureobasidium pullulans and Rhodotorula glutinis were the dominant fungal species, while Enterococcus mundtii (Firmicutes) and Frigoribacterium faeni (Actinobacteria) were the most represented species among bacterial isolates. Enrichment cultures of fresh apricot puree, followed by fermentation trials in beer wort and beer wort added with apricot puree, allowed the selection of four isolates of Pichia kudriavzevii, Hanseniaspora uvarum, H. pseudoguilliermondii, and H. clermontiae able to dominate over the Bisucciu native microbiota and to produce from 0.57% to 0.74% (vol/vol) of ethanol. HS-SPME-GC/MS analysis highlighted a significant increase in the ester and alcohol fractions as well as a reduction in terpenes after fermentation with the selected yeasts. Results obtained suggest that the yeast isolates may contribute to the definition of the taste and flavor of beers when used in mixed fermentations with Saccharomyces.
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Na HE, Heo S, Kim YS, Kim T, Lee G, Lee JH, Jeong DW. The safety and technological properties of Bacillus velezensis DMB06 used as a starter candidate were evaluated by genome analysis. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Kong H, Jeong DW, Kim N, Lee S, Sul S, Lee JH. Safety and Technological Characterization of Staphylococcus xylosus and Staphylococcus pseudoxylosus Isolates from Fermented Soybean Foods of Korea. J Microbiol Biotechnol 2022; 32:458-463. [PMID: 35001006 PMCID: PMC9628813 DOI: 10.4014/jmb.2111.11040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/29/2021] [Accepted: 12/31/2021] [Indexed: 12/15/2022]
Abstract
We evaluated the antibiotic susceptibilities, hemolytic activities, and technological properties of 36 Staphylococcus xylosus strains and 49 S. pseudoxylosus strains predominantly isolated from fermented soybean foods from Korea. Most of the strains were sensitive to chloramphenicol, erythromycin, gentamycin, kanamycin, lincomycin, oxacillin, tetracycline, and trimethoprim. However, 23 strains exhibited potential phenotypic acquired resistance to erythromycin, lincomycin, and tetracycline. Based on breakpoint values for staphylococci from the Clinical and Laboratory Standards Institute, >30% of the isolates were resistant to ampicillin and penicillin G, but the population distributions in minimum inhibitory concentration tests were clearly different from those expected for acquired resistance. None of the strains exhibited clear α- or β-hemolytic activity. S. xylosus and S. pseudoxylosus exhibited salt tolerance on agar medium containing 20% and 22% (w/v) NaCl, respectively. S. xylosus and S. pseudoxylosus strains possessed protease and lipase activities, which were affected by the NaCl concentration. Protease activity of S. pseudoxylosus was strain-specific, but lipase activity might be a characteristic of both species. This study confirms the potential of both species for use in high-salt soybean fermentation, but the safety and technological properties of strains must be determined to select suitable starter candidates.
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Affiliation(s)
- Haram Kong
- Department of Food Science and Biotechnology, Kyonggi University, Suwon 16227, Republic of Korea
| | - Do-Won Jeong
- Department of Food and Nutrition, Dongduk Women’s University, Seoul 02748, Republic of Korea
| | - Namwon Kim
- Department of Food Science and Biotechnology, Kyonggi University, Suwon 16227, Republic of Korea
| | - Sugyeong Lee
- Department of Food Science and Biotechnology, Kyonggi University, Suwon 16227, Republic of Korea
| | - Sooyoung Sul
- Division of Sports Science, Kyonggi University, Suwon 16227, Republic of Korea
| | - Jong-Hoon Lee
- Department of Food Science and Biotechnology, Kyonggi University, Suwon 16227, Republic of Korea
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15
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Transcriptome Analysis of Halotolerant Staphylococcus saprophyticus Isolated from Korean Fermented Shrimp. Foods 2022; 11:foods11040524. [PMID: 35206000 PMCID: PMC8870806 DOI: 10.3390/foods11040524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 11/16/2022] Open
Abstract
Saeu-jeotgal, a Korean fermented shrimp food, is commonly used as an ingredient for making kimchi and other side dishes. The high salinity of the jeotgal contributes to its flavor and inhibits the growth of food spoilage microorganisms. Interestingly, Staphylococcus saprophyticus was discovered to be capable of growth even after treatment with 20% NaCl. To elucidate the tolerance mechanism, a genome-wide gene expression of S. saprophyticus against 0%, 10%, and 20% NaCl was investigated by RNA sequencing. A total of 831, 1314, and 1028 differentially expressed genes (DEGs) were identified in the 0% vs. 10%, 0% vs. 20%, and 10% vs. 20% NaCl comparisons, respectively. The Clusters of Orthologous Groups analysis revealed that the DEGs were involved in amino acid transport and metabolism, transcription, and inorganic ion transport and metabolism. The functional enrichment analysis showed that the expression of the genes encoding mechanosensitive ion channels, sodium/proton antiporters, and betaine/carnitine/choline transporter family proteins was downregulated, whereas the expression of the genes encoding universal stress proteins and enzymes for glutamate, glycine, and alanine synthesis was upregulated. Therefore, these findings suggest that the S. saprophyticus isolated from the saeu-jeotgal utilizes different molecular strategies for halotolerance, with glutamate as the key molecule.
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Genome-based characterization of a plasmid-associated micrococcin P1 biosynthetic gene cluster and virulence factors in Mammaliicoccus sciuri IMDO-S72. Appl Environ Microbiol 2021; 88:e0208821. [PMID: 34936836 DOI: 10.1128/aem.02088-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Analysis of the de novo assembled genome of Mammaliicoccus sciuri IMDO-S72 revealed the genetically encoded machinery behind its earlier reported antibacterial phenotype and gave further insight into the repertoire of putative virulence factors of this recently reclassified species. A plasmid-encoded biosynthetic gene cluster was held responsible for the antimicrobial activity of M. sciuri IMDO-S72, comprising genes involved in thiopeptide production. The compound encoded by this gene cluster was structurally identified as micrococcin P1. Further examination of its genome highlighted the ubiquitous presence of innate virulence factors mainly involved in surface colonization. Determinants contributing to aggressive virulence were generally absent, with exception of a plasmid-associated ica cluster. The native antibiotic resistance genes sal(A) and mecA were detected within the genome, amongst others, but were not consistently linked with a resistant phenotype. While mobile genetic elements were identified within the genome, such as an untypeable SCC element, they proved to be generally free of virulence- and antibiotic-related genes. These results further suggest a commensal lifestyle of M. sciuri and indicate the association of antibiotic resistance determinants with mobile genetic elements, as an important factor in conferring antibiotic resistance, in addition to their unilateral annotation. Importance Mammaliicoccus sciuri has been put forward as an important carrier of virulence and antibiotic resistance genes, which can be transmitted to clinically important staphylococcal species such as Staphylococcus aureus. As a common inhabitant of mammal skin, this species is believed to have a predominant commensal lifestyle although it has been reported as an opportunistic pathogen in some cases. This study provides an extensive genome-wide description of its putative virulence potential taking into consideration the genomic context in which these genes appear, an aspect that is often overlooked during virulence analysis. Additional genome and biochemical analysis linked M. sciuri with the production of micrococcin P1, gaining further insight to which extent these biosynthetic gene cluster are distributed amongst different related species. The frequent plasmid-associated character hints that these traits can be horizontally transferred and might confer a competitive advantage to its recipient within its ecological niche.
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Dimov SG, Gyurova A, Zagorchev L, Dimitrov T, Georgieva-Miteva D, Peykov S. NGS-Based Metagenomic Study of Four Traditional Bulgarian Green Cheeses from Tcherni Vit. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.112278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Settanni L, Busetta G, Puccio V, Licitra G, Franciosi E, Botta L, Di Gerlando R, Todaro M, Gaglio R. In-Depth Investigation of the Safety of Wooden Shelves Used for Traditional Cheese Ripening. Appl Environ Microbiol 2021; 87:e0152421. [PMID: 34550766 PMCID: PMC8579974 DOI: 10.1128/aem.01524-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/13/2021] [Indexed: 01/04/2023] Open
Abstract
The main goal of this research was to characterize the bacterial diversity of the wooden boards used for aging traditional Sicilian cheeses and to evaluate whether pathogenic bacteria are associated with these surfaces. Eighteen cheese dairy factories producing three traditional cheese typologies (PDO Pecorino Siciliano, PDO Piacentinu Ennese, and Caciocavallo Palermitano) were selected within the region of Sicily. The wooden shelf surfaces were sampled by a destructive method to detach wood splinters as well as by a nondestructive brushing to collect microbial cells. Scanning electron microscopy showed the presence of almost continuous bacterial formations on the majority of the shelves analyzed. Yeasts and fungal hyphae were also visualized, indicating the complexity of the plank communities. The amplicon library of the 16S rRNA gene V3-V4 region was paired-end sequenced using the Illumina MiSeq system, allowing the identification of 14 phyla, 32 classes, 52 orders, 93 families, and 137 genera. Staphylococcus equorum was identified from all wooden surfaces, with a maximum abundance of 64.75%. Among cheese-surface-ripening bacteria, Brevibacterium and Corynebacterium were detected in almost all samples. Several halophilic (Halomonas, Tetragenococcus halophilus, Chromohalobacter, Salimicrobium, Marinococcus, Salegentibacter, Haererehalobacter, Marinobacter, and Idiomarinaceae) and moderately halophilic (Salinicoccus, Psychrobacter, and Salinisphaera) bacteria were frequently identified. Lactic acid bacteria (LAB) were present at low percentages in the genera Leuconostoc, Lactococcus, Lactobacillus, Pediococcus, and Streptococcus. The levels of viable microorganisms on the wooden shelves ranged between 2.4 and 7.8 log CFU/cm2. In some cases, LAB were counted at very high levels (8.2 log CFU/cm2). Members of the Enterobacteriaceae family were detected in a viable state for only six samples. Coagulase-positive staphylococci, Salmonella spp., and Listeria monocytogenes were not detected. Seventy-five strains belonged to the genera Leuconostoc, Lactococcus, Pediococcus, Enterococcus, Lactobacillus, and Weissella. IMPORTANCE This study provides evidence for the lack of pathogenic bacteria on the wooden shelves used to ripen internal bacterially ripened semihard and hard cheeses produced in Sicily. These three cheeses are not inoculated on their surfaces, and surface ripening is not considered to occur or, at least, does not occur at the same extent as surface-inoculated smear cheeses. Several bacterial groups identified from the wooden shelves are typically associated with smear cheeses, strongly suggesting that PDO Pecorino Siciliano, PDO Piacentinu Ennese, and Caciocavallo Palermitano cheese rind contributes to their final organoleptic profiles.
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Affiliation(s)
- Luca Settanni
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Gabriele Busetta
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Valeria Puccio
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Giuseppe Licitra
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), Università degli Studi di Catania, Catania, Italy
| | - Elena Franciosi
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all’Adige, Italy
| | - Luigi Botta
- Dipartimento di Ingegneria, UdR INSTM di Palermo, Università degli Studi di Palermo, Palermo, Italy
| | - Rosalia Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Massimo Todaro
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Raimondo Gaglio
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
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Functional Genomic Insights into Probiotic Bacillus siamensis Strain B28 from Traditional Korean Fermented Kimchi. Foods 2021; 10:foods10081906. [PMID: 34441683 PMCID: PMC8394110 DOI: 10.3390/foods10081906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 01/22/2023] Open
Abstract
Bacillus siamensis strain B28 was previously isolated from traditional Korean fermented kimchi and inhibited expression of the microphthalmia-associated transcription factor and β-catenin in human embryonic kidney 293 cells. Here, we determined the complete genome sequence of strain B28 and compared it with other strains to elucidate its potential probiotic properties. Strain B28 does not contain antibiotic resistance-, hemolysin- or enterotoxin-encoding genes. The genome includes genes related to survival in extreme conditions, adhesion in the gut, and synthesis of the bacteriocin. Considering the potential for enhancement of human health, the strain B28 genome encodes genes related to production of eight essential amino acids, γ-aminobutyric acid, branched-chain fatty acids, γ-glutamyltransferase, and subtilisin. There are genes for the synthesis of uracil, lipoteichoic acid, glutathione, and several reactive oxygen species-scavenging enzymes. Experimentally, strain B28 exhibited sensitivity to eight antibiotics and antibacterial activity against seven foodborne pathogens. B. siamensis B28 is a safe strain with potential for development as a probiotic.
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20
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Microbiological Aerosol, Particulate Matter Concentrations and Antibiotic Resistant Staphylococcus spp. in the Premises of Poland’s Oldest Agricultural School. ATMOSPHERE 2021. [DOI: 10.3390/atmos12080934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bioaerosol, particulate matter concentration and antibiotic resistance of airborne Staphylococcus was assessed in animal and public premises (classroom, sports hall, horse stable, cowshed, newborn calf shed and outdoor background control site) of Poland’s oldest agricultural school. The concentration and size distribution of bacteria, fungi, actinomycetes and staphylococci were assessed with a six stage Andersen impactor. Particulate matter (PM10, PM4, PM2.5 and PM1) was determined using the DustTrak aerosol monitor. The Staphylococcus species were determined with MALDI-TOF mass spectrometry and antimicrobial resistance was assessed using disk diffusion. Bioaerosol concentrations differed significantly between sampling points, with the highest levels of all microorganisms occurring in the newborn calf shed. The proportion of respirable fraction exceeded 60% in all sites, indicating potential harmfulness to exposed people. Mean concentrations of particulate matter were the smallest in school rooms and the highest in the newborn calf shed. Neither particulate matter nor microbial aerosol exceeded threshold values for workplaces. Among thirty-four isolated staphylococcal strains, S. equorum (35%), S. succinus (26%) and S. xylosus (15%) were the most prevalent. Resistance to macrolides (erythromycin) and lincosamides (clindamycin) was the most frequent. One strain was methicillin-resistant. Farm animals are significant sources of bioaerosol and therefore attention should be paid with respect to maintaining appropriate sanitary conditions and hygiene of premises and animals.
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21
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Heo S, Kim JH, Kwak MS, Sung MH, Jeong DW. Functional Annotation Genome Unravels Potential Probiotic Bacillus velezensis Strain KMU01 from Traditional Korean Fermented Kimchi. Foods 2021; 10:foods10030563. [PMID: 33803098 PMCID: PMC7998376 DOI: 10.3390/foods10030563] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 12/01/2022] Open
Abstract
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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Affiliation(s)
- Sojeong Heo
- Department of Food and Nutrition, Dongduk Women’s University, Seoul 02748, Korea;
| | - Jong-Hoon Kim
- The Department of Bio and Fermentation Convergence Technology, Kookmin University, Seoul 02707, Korea; (J.-H.K.); (M.-S.K.)
| | - Mi-Sun Kwak
- The Department of Bio and Fermentation Convergence Technology, Kookmin University, Seoul 02707, Korea; (J.-H.K.); (M.-S.K.)
| | - Moon-Hee Sung
- The Department of Bio and Fermentation Convergence Technology, Kookmin University, Seoul 02707, Korea; (J.-H.K.); (M.-S.K.)
- KookminBio Corporation, Seoul 02826, Korea
- Correspondence: or (M.-H.S.); (D.-W.J.); Tel.: +82-2-910-4808 (M.-H.S.); +82-2-940-4463 (D.-W.J.)
| | - Do-Won Jeong
- Department of Food and Nutrition, Dongduk Women’s University, Seoul 02748, Korea;
- Correspondence: or (M.-H.S.); (D.-W.J.); Tel.: +82-2-910-4808 (M.-H.S.); +82-2-940-4463 (D.-W.J.)
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22
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Deimmunized Lysostaphin Synergizes with Small-Molecule Chemotherapies and Resensitizes Methicillin-Resistant Staphylococcus aureus to β-Lactam Antibiotics. Antimicrob Agents Chemother 2021; 65:AAC.01707-20. [PMID: 33318001 DOI: 10.1128/aac.01707-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/06/2020] [Indexed: 12/25/2022] Open
Abstract
There is an urgent need for novel agents to treat drug-resistant bacterial infections, such as multidrug-resistant Staphylococcus aureus (MRSA). Desirable properties for new antibiotics include high potency, narrow species selectivity, low propensity to elicit new resistance phenotypes, and synergy with standard-of-care (SOC) chemotherapies. Here, we describe analysis of the antibacterial potential exhibited by F12, an innovative anti-MRSA lysin that has been genetically engineered to evade detrimental antidrug immune responses in human patients. F12 possesses high potency and rapid onset of action, it has narrow selectivity against pathogenic staphylococci, and it manifests synergy with numerous SOC antibiotics. Additionally, resistance to F12 and β-lactam antibiotics appears mutually exclusive, and, importantly, we provide evidence that F12 resensitizes normally resistant MRSA strains to β-lactams both in vitro and in vivo These results suggest that combinations of F12 and SOC antibiotics are a promising new approach to treating refractory S. aureus infections.
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23
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Heo S, Lee JH, Jeong DW. Food-derived coagulase-negative Staphylococcus as starter cultures for fermented foods. Food Sci Biotechnol 2020; 29:1023-1035. [PMID: 32670656 PMCID: PMC7347722 DOI: 10.1007/s10068-020-00789-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/15/2020] [Accepted: 06/18/2020] [Indexed: 02/07/2023] Open
Abstract
Food safety is of significant concern to consumers and is a major issue for the food industry. As such, the industry is aware of the importance of safety assessments of starters used in the production of fermented foods. Coagulase-negative staphylococci (CNS) are the predominant bacteria found in fermented foods worldwide. Because of this, food-derived CNS are used as starters for cheese and meat fermentation, and have been investigated for use as starters in soybean fermentation. Although food-derived CNS are generally considered non-pathogenic, their safety remains uncertain following the isolation of CNS from skin infections in humans and animals, and because they belong to the same genus as the highly pathogenic species Staphylococcus aureus. This review explores what is known about the safety of food-derived CNS, focusing on antibiotic resistance, enterotoxin genes, and biogenic amine production, to aid in the selection of starter candidates.
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Affiliation(s)
- Sojeong Heo
- Department of Food and Nutrition, Dongduk Women’s University, Seoul, Republic of Korea
| | - Jong-Hoon Lee
- Department of Food Science and Biotechnology, Kyonggi University, Suwon, Republic of Korea
| | - Do-Won Jeong
- Department of Food and Nutrition, Dongduk Women’s University, Seoul, Republic of Korea
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Assessing similarities and disparities in the skin microbiota between wild and laboratory populations of house mice. ISME JOURNAL 2020; 14:2367-2380. [PMID: 32518248 PMCID: PMC7490391 DOI: 10.1038/s41396-020-0690-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 05/15/2020] [Accepted: 05/22/2020] [Indexed: 12/23/2022]
Abstract
The house mouse is a key model organism in skin research including host–microbiota interactions, yet little is known about the skin microbiota of free-living mice. It is similarly unclear how closely laboratory mice, which typically live under exceptionally hygienic conditions, resemble the ancestral state of microbial variation in the wild. In this study, we sampled an area spanning 270 km2 in south-west France and collected 203 wild Mus musculus domesticus. We profiled the ear skin microbiota on standing and active communities (DNA-based and RNA-based 16 rRNA gene sequencing, respectively), and compared multiple community aspects between wild-caught and laboratory-reared mice kept in distinct facilities. Compared to lab mice, we reveal the skin microbiota of wild mice on the one hand to be unique in their composition within the Staphylococcus genus, with a majority of sequences most closely matching known novobiocin-resistant species, and display evidence of a rare biosphere. On the other hand, despite drastic disparities between natural and laboratory environments, we find that shared taxa nonetheless make up the majority of the core skin microbiota of both wild- and laboratory skin communities, suggesting that mammalian skin is a highly specialized habitat capable of strong selection from available species pools. Finally, the influence of environmental factors suggests RNA-based profiling as a preferred method to reduce environmental noise.
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25
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Lopez CM, Callegari ML, Patrone V, Rebecchi A. Assessment of antibiotic resistance in staphylococci involved in fermented meat product processing. Curr Opin Food Sci 2020. [DOI: 10.1016/j.cofs.2019.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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26
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Silencing of Phytopathogen Communication by the Halotolerant PGPR Staphylococcus equorum Strain EN21. Microorganisms 2019; 8:microorganisms8010042. [PMID: 31878301 PMCID: PMC7022284 DOI: 10.3390/microorganisms8010042] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 12/20/2019] [Accepted: 12/22/2019] [Indexed: 12/16/2022] Open
Abstract
Increasing world food demand together with soil erosion and indiscriminate use of chemical fertilization highlight the need to adopt sustainable crop production strategies. In this context, a combination of plant growth-promoting rhizobacteria (PGPR) and pathogen management represents a sustainable and efficient alternative. Though little studied, halophilic and halotolerant PGPR could be a beneficial plant growth promotion strategy for saline and non-saline soils. The virulence of many bacterial phytopathogens is regulated by quorum sensing (QS) systems. Quorum quenching (QQ) involves the enzymatic degradation of phytopathogen-generated signal molecules, mainly N-acyl homoserine lactones (AHLs). In this study, we investigate plant growth-promoting (PGP) activity and the capacity of the halotolerant bacterium Staphylococcus equorum strain EN21 to attenuate phytopathogens virulence through QQ. We used biopriming and in vivo tomato plant experiments to analyse the PGP activity of strain EN21. AHL inactivation was observed to reduce Pseudomonas syringae pv. tomato infections in tomato and Arabidopsis plants. Our study of Dickeya solani, Pectobacterium carotovorum subsp. carotovorum and Erwinia amylovora bacteria in potato tubers, carrots and pears, respectively, also demonstrated the effectiveness of QS interruption by EN21. Overall, this study highlights the potential of strain S. equorum EN21 in plant growth promotion and QQ-driven bacterial phytopathogen biocontrol.
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27
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Stavropoulou DA, De Vuyst L, Leroy F. Nonconventional starter cultures of coagulase-negative staphylococci to produce animal-derived fermented foods, a SWOT analysis. J Appl Microbiol 2018; 125:1570-1586. [PMID: 30053335 DOI: 10.1111/jam.14054] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/15/2018] [Accepted: 07/17/2018] [Indexed: 01/03/2023]
Abstract
Coagulase-negative staphylococci (CNS) are ubiquitous micro-organisms that are commonly present on animal skin and animal-derived foods. They are members of the beneficial microbial consortia of several fermented food products where they contribute to quality. Currently, only a few CNS species are included in commercial starter cultures, although many other ones with promising properties have been isolated from diverse food ecosystems. In the present study, a Strengths-Weaknesses-Opportunities-Threats (SWOT) analysis of the potential use of unconventional CNS starter cultures for the fermentation of animal-derived foods is carried out. An overview of both their desirable and worrisome metabolic traits is given. In general, the application of innovative CNS-based starter cultures offers opportunities to modulate flavour, improve the safety and health aspects and develop novel colour development strategies for clean label products. Yet, their implementation is often not straightforward as nontrivial obstacles or threats are encountered, which relate to technological, food safety and legal concerns. As most of the desirable and undesirable characteristics of CNS species are strain dependent, a case-by-case evaluation is needed when evaluating specific strains for their potential use as novel starter cultures.
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Affiliation(s)
- D A Stavropoulou
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - L De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - F Leroy
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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28
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Lee JH, Heo S, Jeong DW. Genomic insights into Staphylococcus equorum KS1039 as a potential starter culture for the fermentation of high-salt foods. BMC Genomics 2018; 19:136. [PMID: 29433437 PMCID: PMC5810056 DOI: 10.1186/s12864-018-4532-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 02/05/2018] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Our previous comparative genomic analysis of Staphylococcus equorum KS1039 with five S. equorum strains illuminated the genomic basis of its safety and salt tolerance. However, a comprehensive picture of the cellular components and metabolic pathways involved in the degradation of macromolecules and development of sensory properties has not been obtained for S. equorum. Therefore, in this study, we examined the general metabolism of S. equorum based on information obtained from published complete genome sequences of six S. equorum strains isolated from different niches. Additionally, the utility of strain KS1039 as a starter culture for high-salt food fermentations was examined. RESULTS All six S. equorum strains contained genes involved in glycolysis, the tricarboxylic acid cycle, and amino acid metabolic pathways, as well as color development. Moreover, the strains had the potential to produce acetoin, butanediol, and branched chain fatty acids, all of which are important flavor compounds. None of the strains contained decarboxylase genes, which are required for histamine and tyramine production. Strain KS1039 contained bacteriocin and CRISPR/Cas gene clusters, and experimental results suggested that these genes were functional in vitro. CONCLUSIONS The comparative genomic analysis carried out herein provides important information on the usefulness of S. equorum KS1039 as a starter culture for the fermentation of high-salt foods in terms of safety, salt tolerance, bacteriocin production, and foreign plasmid restriction.
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Affiliation(s)
- Jong-Hoon Lee
- Department of Food Science and Biotechnology, Kyonggi University, Suwon, 16227, Republic of Korea
| | - Sojeong Heo
- Department of Food Science and Biotechnology, Kyonggi University, Suwon, 16227, Republic of Korea
- Department of Food and Nutrition, Dongduk Women's University, Seoul, 02748, Republic of Korea
| | - Do-Won Jeong
- Department of Food and Nutrition, Dongduk Women's University, Seoul, 02748, Republic of Korea.
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