1
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Margalho LP, Graça JS, Kamimura BA, Lee SHI, Canales HDS, Chincha AIA, Caturla MYR, Brexó RP, Crucello A, Alvarenga VO, Cruz AG, Oliveira CAF, Sant'Ana AS. Enterotoxigenic Staphylococcus aureus in Brazilian artisanal cheeses: Occurrence, counts, phenotypic and genotypic profiles. Food Microbiol 2024; 121:104531. [PMID: 38637091 DOI: 10.1016/j.fm.2024.104531] [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: 10/13/2023] [Revised: 03/24/2024] [Accepted: 04/02/2024] [Indexed: 04/20/2024]
Abstract
The present study aimed to assess the occurrence and counts of Staphylococcus aureus in Brazilian artisanal cheeses (BAC) produced in five regions of Brazil: Coalho and Manteiga (Northeast region); Colonial and Serrano (South); Caipira (Central-West); Marajó (North); and Minas Artisanal cheeses, from Araxá, Campos das Vertentes, Cerrado, Serro and Canastra microregions (Southeast). The resistance to chlorine-based sanitizers, ability to attach to stainless steel surfaces, and antibiogram profile of a large set of S. aureus strains (n = 585) were assessed. Further, a total of 42 isolates were evaluated for the presence of enterotoxigenic genes (sea, seb, sec, sed, see, seg, sei, sej, and ser) and submitted to typing using pulsed-field gel electrophoresis (PFGE). BAC presented high counts of S. aureus (3.4-6.4 log CFU/g), varying from 25 to 62.5%. From the S. aureus strains (n = 585) assessed, 16% could resist 200 ppm of sodium hypochlorite, whereas 87.6% produced strong ability to attach to stainless steel surfaces, corroborating with S. aureus ability to persist and spread in the environment. Furthermore, the relatively high frequency (80.5%) of multidrug-resistant S. aureus and the presence of enterotoxin genes in 92.6% of the strains is of utmost attention. It reveals the lurking threat of SFP that can survive when conditions are favorable. The presence of enterotoxigenic and antimicrobial-resistant strains of S. aureus in cheese constitutes a potential risk to public health. This result calls for better control of cheese contamination sources, and taking hygienic measures is necessary for food safety. More attention should be paid to animal welfare and hygiene practices in some dairy farms during manufacturing to enhance the microbiological quality of traditional cheese products.
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Affiliation(s)
- Larissa P Margalho
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Juliana S Graça
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Bruna A Kamimura
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Sarah H I Lee
- Department of Food Engineering, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
| | - Héctor D S Canales
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Alexandra I A Chincha
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Magdevis Y R Caturla
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Ramon P Brexó
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Aline Crucello
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Verônica O Alvarenga
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil; Department of Food, Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Adriano G Cruz
- Department of Food, Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Carlos Augusto F Oliveira
- Department of Food Engineering, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
| | - Anderson S Sant'Ana
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil.
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2
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Finton M, Skeie SB, Aspholm ME, Franklin-Alming FV, Mekonnen YB, Kristiansen H, Porcellato D. Two-year investigation of spore-formers through the production chain at two cheese plants in Norway. Food Res Int 2024; 190:114610. [PMID: 38945575 DOI: 10.1016/j.foodres.2024.114610] [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: 02/17/2024] [Revised: 06/04/2024] [Accepted: 06/04/2024] [Indexed: 07/02/2024]
Abstract
Spore-forming bacteria are the most complex group of microbes to eliminate from the dairy production line due to their ability to withstand heat treatment usually used in dairy processing. These ubiquitous microorganisms have ample opportunity for multiple points of entry into the milk chain, creating issues for food quality and safety. Certain spore-formers, namely bacilli and clostridia, are more problematic to the dairy industry due to their possible pathogenicity, growth, and production of metabolites and spoilage enzymes. This research investigated the spore-forming population from raw milk reception at two Norwegian dairy plants through the cheesemaking stages until ripening. Samples were collected over two years and examined by amplicon sequencing in a culture independent manner and after an anaerobic spore-former enrichment step. In addition, a total of 608 isolates from the enriched samples were identified at the genus or species level using MALDI-TOF analysis. Most spore-forming isolates belong to the genera Bacillus or Clostridium, with the latter dominating the enriched MPN tubes of raw milk and bactofugate. Results showed a great variation among the clostridia and bacilli detected in the enriched MPN tubes. However, B. licheniformis and C. tyrobutyricum were identified in all sample types from both plants throughout the 2-year study. In conclusion, our results shed light on the fate of different spore-formers at different processing stages in the cheese production chain, which could facilitate targeted actions to reduce quality problems.
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Affiliation(s)
- Misti Finton
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Siv Borghild Skeie
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Marina Elisabeth Aspholm
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | | | - Yohannes Beyene Mekonnen
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Hanne Kristiansen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
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3
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Shan Q, Wang X, Yang H, Zhu Y, Wang J, Yang G. Bacillus cereus CwpFM induces colonic tissue damage and inflammatory responses through oxidative stress and the NLRP3/NF-κB pathway. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:173079. [PMID: 38735331 DOI: 10.1016/j.scitotenv.2024.173079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/30/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024]
Abstract
Bacillus cereus (B. cereus) from cow milk poses a threat to public health, causing food poisoning and gastrointestinal disorders in humans. We identified CwpFM, an enterotoxin from B. cereus, caused oxidative stress and inflammatory responses in mouse colon and colonic epithelial cells. Colon proteomics revealed that CwpFM elevated proteins associated with inflammation and oxidative stress. Notably, CwpFM induced activation of the NLRP3/NF-κB signaling, but suppressed antioxidant NFE2L2/HO-1 expression in the intestine and epithelial cells. Consistently, CwpFM exposure led to cytotoxicity and ROS accumulation in Caco-2 cells in a dose-dependent manner. Further, NAC (ROS inhibitor) treatment abolished NLRP3/NF-κB activation due to CwpFM. Moreover, overexpression of Nfe2l2 or activation of NFE2L2 by NK-252 reduced ROS production and inhibited activation of the NLRP3/NF-κB pathway. Inhibition of NF-κB by ADPC and/or suppression of NLRP3 by MCC950 attenuated CwpFM-induced inflammatory responses in Caco-2 cells. Collectively, CwpFM induced oxidative stress and NLRP3/NF-κB activation by inhibiting the NFE2L2/HO-1 signaling and ROS accumulation, leading to the development of intestinal inflammation. Our data elucidate the role of oxidative stress and innate immunity in CwpFM enterotoxicity and contribute to developing diagnostic and therapeutic products for B. cereus-related food safety issues.
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Affiliation(s)
- Qiang Shan
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Xue Wang
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Hao Yang
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Yaohong Zhu
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Jiufeng Wang
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; Sanya Institute of China Agricultural University, Sanya 572025, China.
| | - Guiyan Yang
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
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4
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Santamarina-García G, Amores G, Llamazares D, Hernández I, Javier R Barron L, Virto M. Phenotypic and genotypic characterization of antimicrobial resistances reveals the effect of the production chain in reducing resistant lactic acid bacteria in an artisanal raw ewe milk PDO cheese. Food Res Int 2024; 187:114308. [PMID: 38763625 DOI: 10.1016/j.foodres.2024.114308] [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: 01/17/2024] [Revised: 03/27/2024] [Accepted: 04/16/2024] [Indexed: 05/21/2024]
Abstract
Antimicrobial resistance (AMR) is a significant public health threat, with the food production chain, and, specifically, fermented products, as a potential vehicle for dissemination. However, information about dairy products, especially raw ewe milk cheeses, is limited. The present study analysed, for the first time, the occurrence of AMRs related to lactic acid bacteria (LAB) along a raw ewe milk cheese production chain for the most common antimicrobial agents used on farms (dihydrostreptomycin, benzylpenicillin, amoxicillin and polymyxin B). More than 200 LAB isolates were obtained and identified by Sanger sequencing (V1-V3 16S rRNA regions); these isolates included 8 LAB genera and 21 species. Significant differences in LAB composition were observed throughout the production chain (P ≤ 0.001), with Enterococcus (e.g., E. hirae and E. faecalis) and Bacillus (e.g., B. thuringiensis and B. cereus) predominating in ovine faeces and raw ewe milk, respectively, along with Lactococcus (L. lactis) in whey and fresh cheeses, while Lactobacillus and Lacticaseibacillus species (e.g., Lactobacillus sp. and L. paracasei) prevailed in ripened cheeses. Phenotypically, by broth microdilution, Lactococcus, Enterococcus and Bacillus species presented the greatest resistance rates (on average, 78.2 %, 56.8 % and 53.4 %, respectively), specifically against polymyxin B, and were more susceptible to dihydrostreptomycin. Conversely, Lacticaseibacillus and Lactobacillus were more susceptible to all antimicrobials tested (31.4 % and 39.1 %, respectively). Thus, resistance patterns and multidrug resistance were reduced along the production chain (P ≤ 0.05). Genotypically, through HT-qPCR, 31 antimicrobial resistance genes (ARGs) and 6 mobile genetic elements (MGEs) were detected, predominating Str, StrB and aadA-01, related to aminoglycoside resistance, and the transposons tnpA-02 and tnpA-01. In general, a significant reduction in ARGs and MGEs abundances was also observed throughout the production chain (P ≤ 0.001). The current findings indicate that LAB dynamics throughout the raw ewe milk cheese production chain facilitated a reduction in AMRs, which has not been reported to date.
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Affiliation(s)
- Gorka Santamarina-García
- Lactiker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; Bioaraba Health Research Institute-Prevention, Promotion and Health Care, 01009 Vitoria-Gasteiz, Spain; Joint Research Laboratory on Environmental Antibiotic Resistance, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.
| | - Gustavo Amores
- Lactiker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; Bioaraba Health Research Institute-Prevention, Promotion and Health Care, 01009 Vitoria-Gasteiz, Spain; Joint Research Laboratory on Environmental Antibiotic Resistance, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Diego Llamazares
- Lactiker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Igor Hernández
- Lactiker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; Bioaraba Health Research Institute-Prevention, Promotion and Health Care, 01009 Vitoria-Gasteiz, Spain; Joint Research Laboratory on Environmental Antibiotic Resistance, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Luis Javier R Barron
- Lactiker Research Group, Department of Pharmacy and Food Sciences, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; Joint Research Laboratory on Environmental Antibiotic Resistance, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Mailo Virto
- Lactiker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; Bioaraba Health Research Institute-Prevention, Promotion and Health Care, 01009 Vitoria-Gasteiz, Spain; Joint Research Laboratory on Environmental Antibiotic Resistance, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
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5
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Ceciliani F, Maggiolino A, Biscarini F, Dadi Y, De Matos L, Cremonesi P, Landi V, De Palo P, Lecchi C. Heat stress has divergent effects on the milk microbiota of Holstein and Brown Swiss cows. J Dairy Sci 2024:S0022-0302(24)00957-3. [PMID: 38908697 DOI: 10.3168/jds.2024-24976] [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: 03/28/2024] [Accepted: 05/25/2024] [Indexed: 06/24/2024]
Abstract
Heat stress (HS) is one of the pivotal causes of economic losses in dairy industries and affects welfare and performance, but its effect on milk microbiota remains elusive. It is also unclear if and how different breeds may cope with HS in sustaining productive performance. The objectives of this study were to compare a) the performance of 2 dairy breeds, namely Holstein and Brown Swiss, subjected to HS and b) the different effects of HS on the milk microbiota of the 2 breeds in thermal comfort conditions and HS. The study was carried out on 36 dairy cows, 18 per breed. The HS was induced by switching off the cooling system during a natural heat wave for 4 d. Besides the Temperature Humidity Index (THI), the animal stress was confirmed by measuring respiratory frequency and rectal temperature twice daily at 4 a.m. and 3 p.m. The HS differently impacted the 2 breeds. Rectal temperatures were higher in Holstein cows, while no changes in rectal temperature were found in Brown Swiss. Milk yield recording and sampling were performed during the morning milking of d 1 (at 4.00 a.m.) and afternoon milking of d 4 (at 5.00 p.m.). Productive parameters were also different: milk yield, fat-corrected milk, energy-corrected milk, protein and casein content, and renneting parameters were decreased in Holstein but remained unaffected in Brown Swiss. The HS also modified the milk microbiota of the 2 breeds differently. During HS, the Brown Swiss milk microbiota was richer (α diversity) than the Holstein one. Comparing the time points before and during HS within breeds showed that Brown Swiss milk microbiota was less affected by HS than Holstein's. Under the same thermal comfort condition, milk microbiota did not discriminate between Brown Swiss and Holstein. Consistently with α and β diversity, the number of operational taxonomic units (OTUs) at the genus level that changed their abundance during HS was higher in Holstein (74 OTUs) than in Brown Swiss (only 20 OTUs). The most significant changes in abundance affected Acinetobacter, Chryseobacterium, Cutibacterium, Enterococcus, Lactococcus, Prevotella-9, Serratia, and Streptococcus. In conclusion, the present report confirms and extends previous studies by demonstrating that Brown Swiss cows regulate their body temperature better than the Holstein breed. The relative thermal tolerance to HS compared with Holstein is also confirmed by changes in milk uncultured microbiota, which were more evident in Holstein than in Brown Swiss.
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Affiliation(s)
- F Ceciliani
- Department of Veterinary Medicine and Animal Science, Università degli Studi di Milano, via dell'Università 6, 26900 Lodi, Italy
| | - A Maggiolino
- Department of Veterinary Medicine, Università degli Studi di Bari A. Moro, SP per Casamassima, km 3, 70010 - Valenzano BA
| | - F Biscarini
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Milan, Italy
| | - Y Dadi
- Department of Veterinary Medicine and Animal Science, Università degli Studi di Milano, via dell'Università 6, 26900 Lodi, Italy
| | - L De Matos
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Milan, Italy
| | - P Cremonesi
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Milan, Italy
| | - V Landi
- Department of Veterinary Medicine, Università degli Studi di Bari A. Moro, SP per Casamassima, km 3, 70010 - Valenzano BA
| | - P De Palo
- Department of Veterinary Medicine, Università degli Studi di Bari A. Moro, SP per Casamassima, km 3, 70010 - Valenzano BA
| | - C Lecchi
- Department of Veterinary Medicine and Animal Science, Università degli Studi di Milano, via dell'Università 6, 26900 Lodi, Italy.
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6
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Sanschagrin L, Paniconi T, Sanchez Martinez AC, Jubinville E, Goulet-Beaulieu V, Goetz C, Labrie S, Dufour S, Jean J. Identification and Characterization of Microorganisms Isolated from Non-compliant and/or Atypical Dairy Products in Canada. J Dairy Sci 2024:S0022-0302(24)00934-2. [PMID: 38908709 DOI: 10.3168/jds.2023-24506] [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: 12/04/2023] [Accepted: 05/17/2024] [Indexed: 06/24/2024]
Abstract
Despite good manufacturing practices and rigorous cleaning and sanitizing procedures established in dairy processing plants, microbiological contamination remains the main cause of products being non-compliant and/or atypical and hence not fit for human consumption. The objective of this study was to isolate, identify and characterize bacteria, yeasts and molds associated with substandard dairy products in Canada and to create a collection of reference isolates. In addition to conventional microbiological characterization, each isolate was tested for biofilm-forming ability and susceptibility to heat, antimicrobial agents, and common industrial disinfectants. Among the 105 microbial strains isolated from pasteurized milk, cream, and cheese samples, 24 bacterial isolates, belonging mainly to the genus Pseudomonas, were shown to be moderate or strong biofilm producers in 96-well plates and highly resistant to peracetic acid (100 ppm, 5 min contact time) and sodium hypochlorite (70 ppm, 5 min contact time). In addition, 56 bacterial isolates, including Acinetobacter baumannii, Enterobacter bugandensis, Klebsiella pneumoniae and Pseudomonas spp., were found resistant to ampicillin, fosfomycin and/or ceftriaxone, while 14 others, such as Bacillus spp. and Macrococcus spp., withstood a heat treatment equivalent to low-temperature long-time pasteurization (63°C for 30 min). This descriptive study provides new information on potential problematic microorganisms in dairies and will guide the development of novel control strategies intended to prevent and reduce microbiological contamination and the associated economic losses.
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Affiliation(s)
- Laurie Sanschagrin
- Département des sciences des aliments, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada; Centre de recherche en sciences et technologie du lait (STELA), Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, QC, Canada; Regroupement de recherche pour un lait de qualité optimale (Op+lait), Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Teresa Paniconi
- Département des sciences des aliments, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada; Centre de recherche en sciences et technologie du lait (STELA), Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, QC, Canada
| | - Anhely Carolina Sanchez Martinez
- Département des sciences des aliments, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
| | - Eric Jubinville
- Département des sciences des aliments, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada; Centre de recherche en sciences et technologie du lait (STELA), Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, QC, Canada
| | - Valérie Goulet-Beaulieu
- Département des sciences des aliments, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada; Centre de recherche en sciences et technologie du lait (STELA), Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, QC, Canada
| | - Coralie Goetz
- Département des sciences des aliments, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada; Centre de recherche en sciences et technologie du lait (STELA), Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, QC, Canada; Regroupement de recherche pour un lait de qualité optimale (Op+lait), Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Steve Labrie
- Département des sciences des aliments, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada; Centre de recherche en sciences et technologie du lait (STELA), Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, QC, Canada
| | - Simon Dufour
- Regroupement de recherche pour un lait de qualité optimale (Op+lait), Université de Montréal, Saint-Hyacinthe, QC, Canada; Département de pathologie et microbiologie, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Julie Jean
- Département des sciences des aliments, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada; Centre de recherche en sciences et technologie du lait (STELA), Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, QC, Canada; Regroupement de recherche pour un lait de qualité optimale (Op+lait), Université de Montréal, Saint-Hyacinthe, QC, Canada.
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7
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Dean CJ, Deng Y, Wehri TC, Pena-Mosca F, Ray T, Crooker BA, Godden SM, Caixeta LS, Noyes NR. The impact of kit, environment, and sampling contamination on the observed microbiome of bovine milk. mSystems 2024; 9:e0115823. [PMID: 38785438 DOI: 10.1128/msystems.01158-23] [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: 11/06/2023] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
In low-microbial biomass samples such as bovine milk, contaminants can outnumber endogenous bacteria. Because of this, milk microbiome research suffers from a critical knowledge gap, namely, does non-mastitis bovine milk contain a native microbiome? In this study, we sampled external and internal mammary epithelia and stripped and cisternal milk and used numerous negative controls, including air and sampling controls and extraction and library preparation blanks, to identify the potential sources of contamination. Two algorithms were used to mathematically remove contaminants and track the potential movement of microbes among samples. Results suggest that the majority (i.e., >75%) of sequence data generated from bovine milk and mammary epithelium samples represents contaminating DNA. Contaminants in milk samples were primarily sourced from DNA extraction kits and the internal and external skin of the teat, while teat canal and apex samples were mainly contaminated during the sampling process. After decontamination, the milk microbiome displayed a more dispersed, less diverse, and compositionally distinct bacterial profile compared with epithelial samples. Similar microbial compositions were observed between cisternal and stripped milk samples, as well as between teat apex and canal samples. Staphylococcus and Acinetobacter were the predominant genera detected in milk sample sequences, and bacterial culture showed growth of Staphylococcus and Corynebacterium spp. in 50% (7/14) of stripped milk samples and growth of Staphylococcus spp. in 7% (1/14) of cisternal milk samples. Our study suggests that microbiome data generated from milk samples obtained from clinically healthy bovine udders may be heavily biased by contaminants that enter the sample during sample collection and processing workflows.IMPORTANCEObtaining a non-contaminated sample of bovine milk is challenging due to the nature of the sampling environment and the route by which milk is typically extracted from the mammary gland. Furthermore, the very low bacterial biomass of bovine milk exacerbates the impacts of contaminant sequences in downstream analyses, which can lead to severe biases. Our finding showed that bovine milk contains very low bacterial biomass and each contamination event (including sampling procedure and DNA extraction process) introduces bacteria and/or DNA fragments that easily outnumber the native bacterial cells. This finding has important implications for our ability to draw robust conclusions from milk microbiome data, especially if the data have not been subjected to rigorous decontamination procedures. Based on these findings, we strongly urge researchers to include numerous negative controls into their sampling and sample processing workflows and to utilize several complementary methods for identifying potential contaminants within the resulting sequence data. These measures will improve the accuracy, reliability, reproducibility, and interpretability of milk microbiome data and research.
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Affiliation(s)
- C J Dean
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Y Deng
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - T C Wehri
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA
| | - F Pena-Mosca
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - T Ray
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - B A Crooker
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA
| | - S M Godden
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - L S Caixeta
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - N R Noyes
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
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8
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Bücher C, Burtscher J, Zitz U, Domig KJ. One-Year Monitoring of Prevalence and Diversity of Dairy Propionic Acid Bacteria in Raw Milk by Means of Culture-Dependent and Culture-Independent Methods. Foods 2024; 13:1921. [PMID: 38928862 PMCID: PMC11203294 DOI: 10.3390/foods13121921] [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: 05/22/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Even low levels of dairy propionic acid bacteria (dPAB) can cause cheese defects, resulting in severe economic losses for the producers of selected raw milk cheeses. Therefore, routine quality control of raw cheese milk for dPAB contamination is essential if propionic acid fermentation is undesired. Although knowledge of dPAB contamination of raw milk is important to understand cheese spoilage, long-term dPAB screening data are outdated, and studies taking into account different farm management parameters and their potential influence on dPAB levels are scarce. This study aims to provide insight into the dPAB levels of raw milk over time, to identify farm management factors that potentially influence dPAB levels, and to compare a cultural yeast extract lactate agar (YELA) and lithium glycerol agar (LGA) and a culture-independent method (qPCR) for dPAB quantification with respect to their applicability in routine quality control for the dairy industry. For this purpose, bulk tank milk from 25 dairy farms was screened for dPAB contamination over a one-year period. We were able to identify significant differences in the dPAB contamination levels in raw milk depending on selected farm-specific factors and observed relationships between the different types of milking systems and dPAB contamination levels in raw milk. When dPAB were quantified by cultivation on YELA, strong overgrowth of commensal microbiota impeded counting. Therefore, we conclude that quantification on LGA or by qPCR is preferable. Both methods, colony counting on LGA as well as quantification of dPAB using qPCR, have advantages for the application in (routine) quality control of raw milk, one being low-tech and inexpensive, the other being fast and highly specific, but the detection of (low level) dPAB contamination in raw milk remains a challenge.
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Affiliation(s)
- Carola Bücher
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation (FFoQSI), Technopark 1D, 3430 Tulln, Austria;
| | - Johanna Burtscher
- Institute of Food Science, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria; (U.Z.); (K.J.D.)
| | - Ulrike Zitz
- Institute of Food Science, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria; (U.Z.); (K.J.D.)
| | - Konrad J. Domig
- Institute of Food Science, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria; (U.Z.); (K.J.D.)
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9
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Lecaudé C, Orieux N, Chuzeville S, Bertry A, Coissac E, Boyer F, Bonin A, Colomb-Boeckler N, Mathieu B, Recour M, Vindret J, Pignol C, Romand S, Petite C, Taberlet P, Charles C, Bel N, Hauwuy A. Deciphering microbial communities of three Savoyard raw milk cheeses along ripening and regarding the cheese process. Int J Food Microbiol 2024; 418:110712. [PMID: 38723541 DOI: 10.1016/j.ijfoodmicro.2024.110712] [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: 12/15/2023] [Revised: 03/26/2024] [Accepted: 04/17/2024] [Indexed: 05/27/2024]
Abstract
Different Savoyard cheeses are granted with PDO (Protected Designation or Origin) and PGI (Protected Geographical Indication) which guarantees consumers compliance with strict specifications. The use of raw milk is known to be crucial for specific flavor development. To unravel the factors influencing microbial ecosystems across cheese making steps, according to the seasonality (winter and summer) and the mode of production (farmhouse and dairy factory ones), gene targeting on bacteria and fungus was used to have a full picture of 3 cheese making technologies, from the raw milk to the end of the ripening. Our results revealed that Savoyard raw milks are a plenteous source of biodiversity together with the brines used during the process, that may support the development of specific features for each cheese. It was shown that rinds and curds have very contrasted ecosystem diversity, composition, and evolution. Ripening stage was selective for some bacterial species, whereas fungus were mainly ubiquitous in dairy samples. All ripening stages are impacted by the type of cheese technologies, with a higher impact on bacterial communities, except for fungal rind communities, for which the technology is the more discriminant. The specific microorganism's abundance for each technology allow to see a real bar-code, with more or less differences regarding bacterial or fungal communities. Bacterial structuration is shaped mainly by matrices, differently regarding technologies while the influence of technology is higher for fungi. Production types showed 10 differential bacterial species, farmhouses showed more ripening taxa, while dairy factory products showing more lactic acid bacteria. Meanwhile, seasonality looks to be a minor element for the comprehension of both microbial ecosystems, but the uniqueness of each dairy plant is a key explicative feature, more for bacteria than for fungus communities.
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Affiliation(s)
- Cresciense Lecaudé
- CERAQ, Centre de ressources pour l'agriculture de qualité et de montagne, 40 Rue du Terraillet, 73190 Saint-Baldoph, France.
| | - Nicolas Orieux
- ENILV, Ecole Nationale des industries du lait et de la viande, 212Rue Anatole France, 74800 La Roche-sur-Foron, France
| | - Sarah Chuzeville
- ACTALIA, Centre technique d'expertise agroalimentaire, Division d'expertise analytique sur le lait et les produits laitiers, 419 Rte des Champs Laitiers, 74800 Eteaux, France
| | - Alicia Bertry
- ACTALIA, Centre technique d'expertise agroalimentaire, Division d'expertise analytique sur le lait et les produits laitiers, 419 Rte des Champs Laitiers, 74800 Eteaux, France
| | - Eric Coissac
- Université Grenoble Alpes, Université Savoie Mont-Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, 38000 Grenoble, France
| | - Frederic Boyer
- Université Grenoble Alpes, Université Savoie Mont-Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, 38000 Grenoble, France
| | - Aurélie Bonin
- Université Grenoble Alpes, Université Savoie Mont-Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, 38000 Grenoble, France
| | - Nelly Colomb-Boeckler
- ACTALIA, Centre technique d'expertise agroalimentaire, Division d'expertise analytique sur le lait et les produits laitiers, 419 Rte des Champs Laitiers, 74800 Eteaux, France
| | - Bruno Mathieu
- Syndicat Interprofessionnel du Reblochon, 28 Rue Louis Haase, 74230 Thônes, France
| | - Manon Recour
- Syndicat Interprofessionnel du Reblochon, 28 Rue Louis Haase, 74230 Thônes, France
| | - Joël Vindret
- sifa syndicat interprofessionnel du fromage abondance, 16 chemin d'Hirmentaz, 74200 Thonon-les-Bains, France
| | - Céline Pignol
- Savoicime, Syndicat Interprofessionnel de la Tomme de Savoie, 10 Allée Jules Vernes, 74150 Rumilly, France
| | - Stéphane Romand
- Syndicat Interprofessionnel du Reblochon, 28 Rue Louis Haase, 74230 Thônes, France
| | - Caroline Petite
- Syndicat Interprofessionnel de la Tome des Bauges, Rue Henri Bouvier, 73630 Le Chatelard, France
| | - Pierre Taberlet
- Université Grenoble Alpes, Université Savoie Mont-Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, 38000 Grenoble, France
| | - Cécile Charles
- CERAQ, Centre de ressources pour l'agriculture de qualité et de montagne, 40 Rue du Terraillet, 73190 Saint-Baldoph, France
| | - Nadège Bel
- ACTALIA, Centre technique d'expertise agroalimentaire, Division d'expertise analytique sur le lait et les produits laitiers, 419 Rte des Champs Laitiers, 74800 Eteaux, France
| | - Agnès Hauwuy
- CERAQ, Centre de ressources pour l'agriculture de qualité et de montagne, 40 Rue du Terraillet, 73190 Saint-Baldoph, France
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10
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Seyfali E, Khoshtaghaza MH, Rouhi M, Sarlak Z, Najafi G. The potential of pulsed electromagnetic field-generated shock waves for reducing microbial load and improving homogenization in raw milk. Heliyon 2024; 10:e32204. [PMID: 38868044 PMCID: PMC11168425 DOI: 10.1016/j.heliyon.2024.e32204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 05/23/2024] [Accepted: 05/29/2024] [Indexed: 06/14/2024] Open
Abstract
Milk is a highly nutritious food essential for human consumption. However, traditional thermal processing methods can reduce its nutritional value and cause unwanted changes. The use of shock waves produced by pulsed electromagnetic fields (PEMFs) has been explored as a means to reduce pathogenic microorganisms. The effect of shock wave treatment on microbial load and particle distribution in packaged fresh cow's milk was investigated. Additionally, the impact of shock wave treatment on Salmonella enterica counts in a bacterial suspension of phosphate-buffered saline (PBS) was evaluated, as this bacterium is a significant milkborne pathogen. Treatment with 1000 impulses from an electromagnetic shock wave generator resulted in a 0.7-log reduction in the total bacterial count of milk. In a separate experiment, a 300-impulse shock wave treatment applied to a Salmonella enterica suspension achieved a 3-log reduction in bacterial counts. Furthermore, shock wave treatment resulted in a decrease in milk particle size compared to untreated milk. Notably, the volume of milk used in this study aligns with commercially available packaged products, enhancing the experiment's industrial relevance. The use of PEMF to generate shock waves could provide a novel approach for future studies focused on reducing the microbial load of milk and improving its homogenization.
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Affiliation(s)
- Ehsan Seyfali
- Department of Biosystems Engineering, Tarbiat Modares University, Tehran, Iran
| | | | - Milad Rouhi
- Research Center of Oils and Fats, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Zahra Sarlak
- Research Center of Oils and Fats, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Gholamhassan Najafi
- Department of Biosystems Engineering, Tarbiat Modares University, Tehran, Iran
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11
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Zanon T, Franciosi E, Cologna N, Goss A, Mancini A, Gauly M. Alpine grazing management, breed and diet effects on coagulation properties, composition, and microbiota of dairy cow milk by commercial mountain based herds. J Dairy Sci 2024:S0022-0302(24)00913-5. [PMID: 38876212 DOI: 10.3168/jds.2023-24347] [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: 10/25/2023] [Accepted: 05/15/2024] [Indexed: 06/16/2024]
Abstract
Cow milk microbiota has received increased attention in recent years, not only because of its importance for human health but also because of its effect on the quality and technological properties of milk. Several studies, therefore, have investigated the effect of various production factors on the microbial composition of milk. However, most of the previous studies considered a limited number of animals from experimental or single farm, which could have biased the results. Therefore, this study aimed to understand the effect of different alpine production systems on the compositional and microbiological quality of milk, considering commercial herds with different feeding intensities and cattle breeds. The results obtained in this work indicated that the month/season of sampling (July for summer or February for winter) more than farm, breed and cow diet exerted significant effects on cow milk parameters and microbiota. In particular, significant differences were observed for urea content in milk between sampling seasons. Differences in milk fat were mainly related to breed specific effects. From a microbiological point of view, statistically significant differences were found in presumptive lactic acid bacteria counts. Based on a culture-independent method, milk obtained in February harbored the highest number of Firmicutes (e.g., Lactobacillus) and the lowest number of Actinobacteria (e.g., Corynebacterium). Moreover, bacterial richness and diversity were higher in July/summer during alpine pasture season indicating a significant effect of pasture feed on the growth of bacterial communities. The results of this study highlighted the effect of month/season mainly related to differences in feeding management (e.g., access to pasture during vegetation period, concentrates supplementation) on composition and microbiota in milk.
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Affiliation(s)
- Thomas Zanon
- Free University of Bolzano (Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, Piazza Università 5, 39100 Bolzano, Italy).
| | - Elena Franciosi
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all'Adige, 38010 San Michele all'Adige (TN), Italy
| | - Nicola Cologna
- Trentingrana Consorzio dei Caseifici Sociali Trentini s.c.a., Via Bregenz 18, Trento, Italy
| | - Andrea Goss
- Trentingrana Consorzio dei Caseifici Sociali Trentini s.c.a., Via Bregenz 18, Trento, Italy
| | - Andrea Mancini
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all'Adige, 38010 San Michele all'Adige (TN), Italy
| | - Matthias Gauly
- Free University of Bolzano (Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, Piazza Università 5, 39100 Bolzano, Italy)
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12
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Zhang Y, Yu P, Tao F. Dynamic Interplay between Microbiota Shifts and Differential Metabolites during Dairy Processing and Storage. Molecules 2024; 29:2745. [PMID: 38930811 PMCID: PMC11206652 DOI: 10.3390/molecules29122745] [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: 03/10/2024] [Revised: 05/25/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Due to the intricate complexity of the original microbiota, residual heat-resistant enzymes, and chemical components, identifying the essential factors that affect dairy quality using traditional methods is challenging. In this study, raw milk, pasteurized milk, and ultra-heat-treated (UHT) milk samples were collectively analyzed using metagenomic next-generation sequencing (mNGS), high-throughput liquid chromatography-mass spectrometry (LC-MS), and gas chromatography-mass spectrometry (GC-MS). The results revealed that raw milk and its corresponding heated dairy products exhibited different trends in terms of microbiota shifts and metabolite changes during storage. Via the analysis of differences in microbiota and correlation analysis of the microorganisms present in differential metabolites in refrigerated pasteurized milk, the top three differential microorganisms with increased abundance, Microbacterium (p < 0.01), unclassified Actinomycetia class (p < 0.05), and Micrococcus (p < 0.01), were detected; these were highly correlated with certain metabolites in pasteurized milk (r > 0.8). This indicated that these genera were the main proliferating microorganisms and were the primary genera involved in the metabolism of pasteurized milk during refrigeration-based storage. Microorganisms with decreased abundance were classified into two categories based on correlation analysis with certain metabolites. It was speculated that the heat-resistant enzyme system of a group of microorganisms with high correlation (r > 0.8), such as Pseudomonas and Acinetobacter, was the main factor causing milk spoilage and that the group with lower correlation (r < 0.3) had a lower impact on the storage process of pasteurized dairy products. By comparing the metabolic pathway results based on metagenomic and metabolite annotation, it was proposed that protein degradation may be associated with microbial growth, whereas lipid degradation may be linked to raw milk's initial heat-resistant enzymes. By leveraging the synergy of metagenomics and metabolomics, the interacting factors determining the quality evolution of dairy products were systematically investigated, providing a novel perspective for controlling dairy processing and storage effectively.
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Affiliation(s)
- Yinan Zhang
- Key Laboratory of Milk and Dairy Products Detection and Monitoring Technology for State Market Regulation, Shanghai Institute of Quality Inspection and Technical Research, Shanghai 200233, China
| | - Peng Yu
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai 200436, China;
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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13
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Morandi S, Silvetti T, Lopreiato V, Piccioli-Cappelli F, Trevisi E, Brasca M. Biodiversity and antibiotic resistance profile provide new evidence for a different origin of enterococci in bovine raw milk and feces. Food Microbiol 2024; 120:104492. [PMID: 38431334 DOI: 10.1016/j.fm.2024.104492] [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: 09/14/2022] [Revised: 01/25/2024] [Accepted: 02/14/2024] [Indexed: 03/05/2024]
Abstract
Enterococci are widely distributed in dairy sector. They are commensals of the gastrointestinal tract of animals, thus, via fecal contamination, could reach raw milk and dairy products. The aims of this study were: 1) to investigate the enterococcal diversity in cow feces and milk samples and 2) to evaluate the antibiotic resistance (AR) of dairy-related enterococci and their ability to transfer resistance genes. E. faecalis (59.9%), E. faecium (18.6%) and E. lactis (12.4%) were prevalent in milk, while E. faecium (84.2%) and E. hirae (15.0%) were dominant in bovine feces. RAPD-PCR highlighted a high number of Enterococcus biotypes (45 from milk and 37 from feces) and none of the milk strains exhibited genetic profiles similar to those of feces biotypes. A high percentage of enterococci isolated from milk (71%) were identified as multidrug resistant and resistance against streptomycin and tetracycline were widespread among milk strains while enterococci from feces were commonly resistant to linezolid and quinupristin/dalfopristin. Only E. faecalis strains were able to transfer horizontally the tetM gene to Lb. delbrueckii subsp. lactis. Our results indicated that Enterococcus biotypes from milk and bovine feces belong to different community and the ability of these microorganisms to transfer AR genes is strain-dependent.
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Affiliation(s)
- Stefano Morandi
- Institute of Sciences of Food Production (ISPA), Italian National Research Council, Milan, Italy.
| | - Tiziana Silvetti
- Institute of Sciences of Food Production (ISPA), Italian National Research Council, Milan, Italy
| | - Vincenzo Lopreiato
- Department of Veterinary Sciences, University of Messina, Viale Palatucci 13, Messina, 98168, Italy
| | - Fiorenzo Piccioli-Cappelli
- Department of Animal Sciences, Food and Nutrition (DIANA), Alimentari e Ambientali, Università Cattolica Del Sacro Cuore, Piacenza, 29122, Italy
| | - Erminio Trevisi
- Department of Animal Sciences, Food and Nutrition (DIANA), Alimentari e Ambientali, Università Cattolica Del Sacro Cuore, Piacenza, 29122, Italy
| | - Milena Brasca
- Institute of Sciences of Food Production (ISPA), Italian National Research Council, Milan, Italy
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14
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Paiva NML, Ribeiro SC, Rosa HJD, Silva CCG. Comparative study of the bacterial community of organic and conventional cow's milk. Food Microbiol 2024; 120:104488. [PMID: 38431314 DOI: 10.1016/j.fm.2024.104488] [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: 11/15/2023] [Revised: 02/01/2024] [Accepted: 02/04/2024] [Indexed: 03/05/2024]
Abstract
Agricultural practises such as conventional and organic farming can potentially affect the microbial communities in milk. In the present study, the bacterial diversity of milk was investigated using high-throughput sequencing on ten organic and ten conventional farms in the Azores, a region where milk production is largely based on year-round grazing systems. The microbiota of milk from both production systems was dominated by Bacillota, Pseudomonadota, Actinomycetota and Bacteroidota. The organic milk showed greater heterogeneity between farms, as reflected in the dispersion of diversity indices and the large variation in the relative abundances of the dominant genera. In contrast, conventionally produced milk showed a high degree of similarity within each season. In the conventional production system, the season also had a strong influence on the bacterial community, but this effect was not observed in the organic milk. The LEfSe analysis identified the genus Iamia as significantly (p < 0.05) more abundant in organic milk, but depending on the season, several other genera were identified that distinguished organic milk from conventionally produced milk. Of these, Bacillus, Iamia and Nocardioides were associated with the soil microbiota in organic farming.
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Affiliation(s)
- Nuno M L Paiva
- School of Agrarian and Environmental Sciences, University of the Azores, Angra do Heroísmo, Azores, Portugal
| | - Susana C Ribeiro
- Institute of Agricultural and Environmental Research and Technology (IITAA), University of the Azores, Angra do Heroísmo, Azores, Portugal
| | - Henrique J D Rosa
- School of Agrarian and Environmental Sciences, University of the Azores, Angra do Heroísmo, Azores, Portugal; Institute of Agricultural and Environmental Research and Technology (IITAA), University of the Azores, Angra do Heroísmo, Azores, Portugal
| | - Célia C G Silva
- School of Agrarian and Environmental Sciences, University of the Azores, Angra do Heroísmo, Azores, Portugal; Institute of Agricultural and Environmental Research and Technology (IITAA), University of the Azores, Angra do Heroísmo, Azores, Portugal.
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15
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Jiang Y, Pan Y, Yin J. Prevalence, toxin-genotype distribution, and transmission of Clostridium perfringens from the breeding and milking process of dairy farms. Food Microbiol 2024; 120:104485. [PMID: 38431330 DOI: 10.1016/j.fm.2024.104485] [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: 11/19/2023] [Revised: 01/03/2024] [Accepted: 02/03/2024] [Indexed: 03/05/2024]
Abstract
This study aimed to elucidate the distribution, transmission, and cross-contamination of Clostridium perfringens during the breeding and milking process from dairy farms. The prevalence of 22.3% (301/1351) yielded 494 C. perfringens isolates; all isolates were type A, except for one type D, and 69.8% (345/494) of the isolates carried atyp. cpb2 and only 0.6% (3/494) of the isolates carried cons. cpb2. C. perfringens detected throughout the whole process but without type F. 150 isolates were classified into 94 pulsed-field gel electrophoresis (PFGE) genotypes; among them, six clusters contained 34 PFGE genotypes with 58.0% isolates which revealed epidemic correlation and genetic diversity; four PFGE genotypes (PT57, PT9, PT61, and PT8) were the predominant genotypes. The isolates from different farms demonstrated high homology. Our study confirmed that C. perfringens demonstrated broad cross-contamination from nipples and hides of dairy cattle, followed by personnel and tools and air-introduced raw milk during the milking process. In conclusion, raw milk could serve as a medium for the transmission of C. perfringens, which could result in human food poisoning. Monitoring and controlling several points of cross-contamination during the milking process are essential as is implementing stringent hygiene measures to prevent further spread and reduce the risk of C. perfringens infection.
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Affiliation(s)
- Yanfen Jiang
- College of Veterinary Medicine, Northwest A&F University, 712100, Yangling, Shaanxi, China.
| | - Yifan Pan
- College of Food Science and Engineering, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Jingyi Yin
- College of Veterinary Medicine, Northwest A&F University, 712100, Yangling, Shaanxi, China
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16
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Kreinin Y, Talmon Y, Levi M, Khoury M, Or I, Raad M, Bolotin G, Sznitman J, Korin N. A Fibrin-Thrombin Based In Vitro Perfusion System to Study Flow-Related Prosthetic Heart Valves Thrombosis. Ann Biomed Eng 2024; 52:1665-1677. [PMID: 38459196 PMCID: PMC11082030 DOI: 10.1007/s10439-024-03480-6] [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: 11/02/2023] [Accepted: 02/20/2024] [Indexed: 03/10/2024]
Abstract
Prosthetic heart valve (PHV) replacement has increased the survival rate and quality of life for heart valve-diseased patients. However, PHV thrombosis remains a critical problem associated with these procedures. To better understand the PHV flow-related thrombosis problem, appropriate experimental models need to be developed. In this study, we present an in vitro fibrin clot model that mimics clot accumulation in PHVs under relevant hydrodynamic conditions while allowing real-time imaging. We created 3D-printed mechanical aortic valve models that were inserted into a transparent glass aorta model and connected to a system that simulates human aortic flow pulse and pressures. Thrombin was gradually injected into a circulating fibrinogen solution to induce fibrin clot formation, and clot accumulation was quantified via image analysis. The results of valves positioned in a normal versus a tilted configuration showed that clot accumulation correlated with the local flow features and was mainly present in areas of low shear and high residence time, where recirculating flows are dominant, as supported by computational fluid dynamic simulations. Overall, our work suggests that the developed method may provide data on flow-related clot accumulation in PHVs and may contribute to exploring new approaches and valve designs to reduce valve thrombosis.
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Affiliation(s)
- Yevgeniy Kreinin
- Department of Biomedical Engineering, Technion-IIT, 3200003, Haifa, Israel
| | - Yahel Talmon
- Department of Biomedical Engineering, Technion-IIT, 3200003, Haifa, Israel
| | - Moran Levi
- Department of Biomedical Engineering, Technion-IIT, 3200003, Haifa, Israel
| | - Maria Khoury
- Department of Biomedical Engineering, Technion-IIT, 3200003, Haifa, Israel
| | - Itay Or
- Department of Cardiac Surgery, Rambam Health Care Campus, 3109601, Haifa, Israel
| | - Mahli Raad
- Department of Cardiac Surgery, Rambam Health Care Campus, 3109601, Haifa, Israel
| | - Gil Bolotin
- Department of Cardiac Surgery, Rambam Health Care Campus, 3109601, Haifa, Israel
- The Ruth Bruce Rappaport Faculty of Medicine, Technion-IIT, 3525433, Haifa, Israel
| | - Josué Sznitman
- Department of Biomedical Engineering, Technion-IIT, 3200003, Haifa, Israel
| | - Netanel Korin
- Department of Biomedical Engineering, Technion-IIT, 3200003, Haifa, Israel.
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17
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Tayyarcan EK, Evran E, Guven K, Ekiz E, Acar Soykut E, Boyaci IH. Evaluating the efficacy of a phage cocktail against Pseudomonas fluorescens group strains in raw milk: microbiological, physical, and chemical analyses. Arch Microbiol 2024; 206:283. [PMID: 38806864 DOI: 10.1007/s00203-024-04008-1] [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: 04/04/2024] [Revised: 05/02/2024] [Accepted: 05/16/2024] [Indexed: 05/30/2024]
Abstract
The objective of this study was to investigate the effectiveness of a phage cocktail against Pseudomonas fluorescens group and its effect on the microbial, physical and chemical properties of raw milk during different storage conditions. A phage cocktail consisting of Pseudomonas fluorescens, Pseudomonas tolaasii, and Pseudomonas libanensis phages was prepared. As a result, reductions in fluorescent Pseudomonas counts of up to 3.44 log units for the storage at 4 °C and 2.38 log units for the storage at 25 °C were achieved. Following the phage application, it is found that there was no significant difference in the total mesophilic aerobic bacteria and Enterobacteriaceae counts. However, it was observed that the number of lactic acid bacteria was higher in phage-treated groups. The results also showed that pH values in the phage added groups were lower than the others and the highest titratable acidity was obtained only in the bacteria-inoculated group. As a future perspective, this study suggests that, while keeping the number of target microorganisms under control in the milk with the use of phages during storage, the microbiota and accordingly the quality parameters of the milk can be affected. This work contributes to the development of effective strategies for maintaining the quality and extending the shelf life of milk and dairy products.
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Affiliation(s)
| | - Eylul Evran
- Food Engineering Department, Hacettepe University, Beytepe, Ankara, Turkey
| | - Kubra Guven
- Food Engineering Department, Hacettepe University, Beytepe, Ankara, Turkey
| | - Esra Ekiz
- Food Engineering Department, Hacettepe University, Beytepe, Ankara, Turkey
| | - Esra Acar Soykut
- Food Engineering Department, Bolu Abant Izzet Baysal University, Bolu, Turkey
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18
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Forouzani‐Moghaddam MJ, Habibi S, Hosseini‐Safa A, Khanaliha K, Mokarinejad R, Akhoundzadeh F, Oshaghi M. Rapid detection of major enterotoxin genes and antibiotic resistance of Staphylococcus aureus isolated from raw milk in the Yazd province, Iran. Vet Med Sci 2024; 10:e1407. [PMID: 38519836 PMCID: PMC10959825 DOI: 10.1002/vms3.1407] [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: 07/20/2023] [Revised: 01/22/2024] [Accepted: 02/19/2024] [Indexed: 03/25/2024] Open
Abstract
INTRODUCTION Raw milk is a nutrient-rich food, but it may harbour harmful bacteria, such as enterotoxigenic Staphylococcus aureus (S. aureus), which can cause staphylococcal food poisoning. Antibiotic resistance of S. aureus in raw milk can increase the risk of such infections, particularly among susceptible individuals. OBJECTIVE This study aimed to investigate the prevalence of enterotoxin genes a, d, g, i and j and the antibiotic resistance of S. aureus isolated from raw milk samples. METHODS During a 6-month sampling period, 60 raw milk specimens were obtained from diverse locations in Yazd province, Iran. Antibiogram profiling was conducted via the disc diffusion method. In addition, staphylococcal enterotoxin (SE) genes a, d, g, i, and j were detected through real-time PCR analysis. RESULTS Bacteriological assays confirmed the presence of S. aureus in 11 samples (18.3%). All isolates demonstrated 100% resistance to penicillin G but exhibited sensitivity to vancomycin, while resistance to other antibiotics ranged from 36.4% to 45.5%. The prevalence of enterotoxin genes in these strains showed variable distribution, with sea being the predominant SE (45.5%), followed by sed (36.4%), seg (18.2), sej and sei (9.1% each). CONCLUSIONS This study discovered the presence of multiple enterotoxins in S. aureus strains obtained from raw milk samples. These strains also demonstrated resistance to a variety of antibiotics. Since enterotoxigenic S. aureus is known to cause human food poisoning, monitoring food hygiene practices, especially during raw milk production, is critical.
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Affiliation(s)
| | - Sina Habibi
- Department of Medical Laboratory SciencesFaculty of Allied MedicineIran University of Medical SciencesTehranIran
- Department of Hematology and Blood Banking, Faculty of Allied MedicineIran University of Medical SciencesTehranIran
| | - Ahmad Hosseini‐Safa
- Department of Medical Laboratory SciencesFaculty of Allied MedicineIran University of Medical SciencesTehranIran
| | - Khadijeh Khanaliha
- Research Center of Pediatric Infectious DiseasesInstitute of Immunology and Infectious DiseasesIran University of Medical SciencesTehranIran
| | - Roya Mokarinejad
- Department of Medical Laboratory SciencesFaculty of Allied MedicineIran University of Medical SciencesTehranIran
| | - Fatemeh Akhoundzadeh
- Department of Medical Laboratory SciencesFaculty of Allied MedicineIran University of Medical SciencesTehranIran
| | - Mojgan Oshaghi
- Department of Medical Laboratory SciencesFaculty of Allied MedicineIran University of Medical SciencesTehranIran
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19
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Guo W, Liu S, Khan MZ, Wang J, Chen T, Alugongo GM, Li S, Cao Z. Bovine milk microbiota: Key players, origins, and potential contributions to early-life gut development. J Adv Res 2024; 59:49-64. [PMID: 37423549 PMCID: PMC11081965 DOI: 10.1016/j.jare.2023.06.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/11/2023] Open
Abstract
BACKGROUND Bovine milk is a significant substitute for human breast milk and holds great importance in infant nutrition and health. Apart from essential nutrients, bovine milk also contains bioactive compounds, including a microbiota derived from milk itself rather than external sources of contamination. AIM OF REVIEW Recognizing the profound impact of bovine milk microorganisms on future generations, our review focuses on exploring their composition, origins, functions, and applications. KEY SCIENTIFIC CONCEPTS OF REVIEW Some of the primary microorganisms found in bovine milk are also present in human milk. These microorganisms are likely transferred to the mammary gland through two pathways: the entero-mammary pathway and the rumen-mammary pathway. We also elucidated potential mechanisms by which milk microbiota contribute to infant intestinal development. The mechanisms include the enhancing of the intestinal microecological niche, promoting the maturation of immune system, strengthening the intestinal epithelial barrier function, and interacting with milk components (e.g., oligosaccharides) via cross-feeding effect. However, given the limited understanding of bovine milk microbiota, further studies are necessary to validate hypotheses regarding their origins and to explore their functions and potential applications in early intestinal development.
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Affiliation(s)
- Wenli Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shuai Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Muhammad Z Khan
- Faculty of Veterinary and Animal Sciences, Department of Animal Breeding and Genetics, The University of Agriculture, Dera Ismail Khan 29220, Pakistan
| | - Jingjun Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Tianyu Chen
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Gibson M Alugongo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shengli Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhijun Cao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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20
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Paula VB, Dias LG, Estevinho LM. Microbiological and Physicochemical Evaluation of Hydroxypropyl Methylcellulose (HPMC) and Propolis Film Coatings for Cheese Preservation. Molecules 2024; 29:1941. [PMID: 38731432 PMCID: PMC11085808 DOI: 10.3390/molecules29091941] [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: 03/13/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 05/13/2024] Open
Abstract
Dairy products are highly susceptible to contamination from microorganisms. This study aimed to evaluate the efficacy of hydroxypropyl methylcellulose (HPMC) and propolis film as protective coatings for cheese. For this, microbiological analyses were carried out over the cheese' ripening period, focusing on total mesophilic bacteria, yeasts and moulds, lactic acid bacteria, total coliforms, Escherichia coli, and Enterobacteriaceae. Physicochemical parameters (pH, water activity, colour, phenolic compounds content) were also evaluated. The statistical analysis (conducted using ANOVA and PERMANOVA) showed a significant interaction term between the HPMC film and propolis (factor 1) and storage days (factor 2) with regard to the dependent variables: microbiological and physicochemical parameters. A high level of microbial contamination was identified at the baseline. However, the propolis films were able to reduce the microbial count. Physicochemical parameters also varied with storage time, with no significant differences found for propolis-containing films. Overall, the addition of propolis to the film influenced the cheeses' colour and the quantification of phenolic compounds. Regarding phenolic compounds, their loss was verified during storage, and was more pronounced in films with a higher percentage of propolis. The study also showed that, of the three groups of phenolic compounds (hydroxybenzoic acids, hydroxycinnamic acids, and flavonoids), hydroxycinnamic acids showed the most significant losses. Overall, this study reveals the potential of using HPMC/propolis films as a coating for cheese in terms of microbiological control and the preservation of physicochemical properties.
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Affiliation(s)
- Vanessa B. Paula
- Doctoral School, University of León (ULE), Campus de Vegazana, 24007 León, Spain
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, 5300-253 Bragança, Portugal; (L.G.D.); (L.M.E.)
| | - Luís G. Dias
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, 5300-253 Bragança, Portugal; (L.G.D.); (L.M.E.)
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Letícia M. Estevinho
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, 5300-253 Bragança, Portugal; (L.G.D.); (L.M.E.)
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
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21
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Cohen A, Turjeman S, Levin R, Tal S, Koren O. Comparison of canine colostrum and milk using a multi-omics approach. Anim Microbiome 2024; 6:19. [PMID: 38650014 PMCID: PMC11034113 DOI: 10.1186/s42523-024-00309-4] [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: 09/04/2023] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND A mother's milk is considered the gold standard of nutrition in neonates and is a source of cytokines, immunoglobulins, growth factors, and other important components, yet little is known about the components of canine milk, specifically colostrum, and the knowledge related to its microbial and metabolic profiles is particularly underwhelming. In this study, we characterized canine colostrum and milk microbiota and metabolome for several breeds of dogs and examined profile shifts as milk matures in the first 8 days post-whelping. RESULTS Through untargeted metabolomics, we identified 63 named metabolites that were significantly differentially abundant between days 1 and 8 of lactation. Surprisingly, the microbial compositions of the colostrum and milk, characterized using 16S rRNA gene sequencing, were largely similar, with only two differentiating genera. The shifts observed, mainly increases in several sugars and amino sugars over time and shifts in amino acid metabolites, align with shifts observed in human milk samples and track with puppy development. CONCLUSION Like human milk, canine milk composition is dynamic, and shifts are well correlated with developing puppies' needs. Such a study of the metabolic profile of canine milk, and its relation to the microbial community, provides insights into the changing needs of the neonate, as well as the ideal nutrition profile for optimal functionality. This information will add to the existing knowledge base of canine milk composition with the prospect of creating a quality, tailored milk substitute or supplement for puppies.
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Affiliation(s)
- Alisa Cohen
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Sondra Turjeman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Rachel Levin
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Smadar Tal
- Koret School of Veterinary Medicine, The Hebrew University Veterinary Teaching Hospital, Hebrew University of Jerusalem, Rehovot, Israel
- Tel-Hai Academic College, Upper Galilee, Israel
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.
- Kyung Hee University, Seoul, the Republic of Korea.
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22
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Vacca M, Celano G, Serale N, Costantino G, Calabrese FM, Calasso M, De Angelis M. Dynamic microbial and metabolic changes during Apulian Caciocavallo cheese-making and ripening produced according to a standardized protocol. J Dairy Sci 2024:S0022-0302(24)00750-1. [PMID: 38642657 DOI: 10.3168/jds.2023-24049] [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: 08/04/2023] [Accepted: 03/12/2024] [Indexed: 04/22/2024]
Abstract
The cheese microbiota plays a critical role in influencing its sensory and physicochemical properties. In this study, traditional Apulian Caciocavallo cheese coming from 4 different dairies in the same area and produced following standardized procedures have been examined, as well as the different bulk milks and natural whey starter cultures used. Moreover, considering the cheese wheels as the blocks of Caciocavallo cheeses as whole, these were characterized at different layers (i.e., core, under-rind, and rind) of the block using a multi-omics approach. In addition to physical-chemical characterization, culturomics, quantitative PCR, metagenomics, and metabolomics analysis, have been carried out post-salting and throughout ripening time (2 mo) to investigate the major shifts in the succession of the microbiota and flavor development. Culture-dependent and 16S rRNA metataxonomics results clearly clustered samples based on the microbiota biodiversity related to the production dairy plant as the result of the use of different NWS or intrinsic conditions of each production site. At the beginning of the ripening, cheeses were dominated by the Lactobacillus and, in 2 dairies (Art and SdC), Streptococcus genera associated with the NWS. The analysis allowed us to show that, although the diversity of identified genera did not change significantly between the rind, under-rind and core fractions of the same samples, there was an evolution in the relative abundance and absolute quantification, modifying and differentiating profiles during ripening. The qPCR mainly differentiated the temporal adaptation of those species originating from bulk milks and those provided by NWSs. The primary starter detected in NWS and cheese reassured the high relative concentration of 1-butanol, 2-butanol, 2-heptanol, 2-butanone, acetoin, delta-dodecalactone, hexanoic acid ethyl ester, octanoic acid ethyl ester, and VFFA during ripening, while cheeses displaying low abundances of Streptococcus and Lactococcus (dairy Del) have a lower total concentration of acetoin compared with Art and SdC. However, the sub-dominant strains and NSLAB present in cheeses are responsible for the production of secondary metabolites belonging to the chemical classes of ketones, alcohols, and organic acids, reaffirming the importance and relevance of autochthonous strains of each dairy plant although considering a delimited production area.
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Affiliation(s)
- Mirco Vacca
- Dept. of Soil, Plant and Food Science (DiSSPA), University of Bari Aldo Moro, via G. Amendola 165/A, 70126, Bari, Italy
| | - Giuseppe Celano
- Dept. of Soil, Plant and Food Science (DiSSPA), University of Bari Aldo Moro, via G. Amendola 165/A, 70126, Bari, Italy.
| | - Nadia Serale
- Dept. of Soil, Plant and Food Science (DiSSPA), University of Bari Aldo Moro, via G. Amendola 165/A, 70126, Bari, Italy
| | - Giuseppe Costantino
- Dept. of Soil, Plant and Food Science (DiSSPA), University of Bari Aldo Moro, via G. Amendola 165/A, 70126, Bari, Italy
| | - Francesco Maria Calabrese
- Dept. of Soil, Plant and Food Science (DiSSPA), University of Bari Aldo Moro, via G. Amendola 165/A, 70126, Bari, Italy
| | - Maria Calasso
- Dept. of Soil, Plant and Food Science (DiSSPA), University of Bari Aldo Moro, via G. Amendola 165/A, 70126, Bari, Italy.
| | - Maria De Angelis
- Dept. of Soil, Plant and Food Science (DiSSPA), University of Bari Aldo Moro, via G. Amendola 165/A, 70126, Bari, Italy
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23
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Yap M, O'Sullivan O, O'Toole PW, Sheehan JJ, Fenelon MA, Cotter PD. Seasonal and geographical impact on the Irish raw milk microbiota correlates with chemical composition and climatic variables. mSystems 2024; 9:e0129023. [PMID: 38445870 PMCID: PMC11019797 DOI: 10.1128/msystems.01290-23] [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: 12/01/2023] [Accepted: 02/14/2024] [Indexed: 03/07/2024] Open
Abstract
Season and location have previously been shown to be associated with differences in the microbiota of raw milk, especially in milk from pasture-based systems. Here, we further advance research in this area by examining differences in the raw milk microbiota from several locations across Ireland over 12 months, and by investigating microbiota associations with climatic variables and chemical composition. Shotgun metagenomic sequencing was used to investigate the microbiota of raw milk collected from nine locations (n = 241). Concurrent chemical analysis of the protein, fat, lactose, total solids, nonprotein nitrogen contents, and titratable acidity (TA) of the same raw milk were performed. Although the raw milk microbiota was highly diverse, a core microbiota was found, with Pseudomonas_E, Lactococcus, Acinetobacter, and Leuconostoc present in all samples. Microbiota diversity significantly differed by season and location, with differences in seasonality and geography corresponding to 11.8% and 10.5% of the variation in the microbiota. Functional and antibiotic resistance profiles also varied across season and location. The analysis of other metadata revealed additional interactions, such as an association between mean daily air and grass temperatures with the abundance of spoilage taxa like Pseudomonas species. Correlations were identified between pathogenic, mastitis-related species, fat content, and the number of sun hours, suggesting a seasonal effect. Ultimately, this study expands our understanding of the interconnected nature of the microbiota, environment/climate variables, and chemical composition of raw milk and provides evidence of a season- and location-specific microbiota. IMPORTANCE The microbiota of raw milk is influenced by many factors that encourage or prevent the introduction and growth of both beneficial and undesirable microorganisms. The seasonal and geographical impacts on the microbial communities of raw milk have been previously seen, but the relationships with environmental factors and the chemical composition has yet to be investigated. In this year-long study, we found that while raw milk is highly diverse, a core microbiota was detected for Irish raw milk, with strong evidence of seasonal and geographical influence. We also found associations between groups of microorganisms, environmental factors, and milk composition, which expand current knowledge on the relationships between microbial and chemical composition and the climate. These results provide evidence for the development of a tool to allow for the prediction of raw milk quality and safety.
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Affiliation(s)
- Min Yap
- Teagasc Food Research Centre, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Orla O'Sullivan
- Teagasc Food Research Centre, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
- VistaMilk SFI Research Centre, Cork, Ireland
| | - Paul W. O'Toole
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Jeremiah J. Sheehan
- Teagasc Food Research Centre, Cork, Ireland
- VistaMilk SFI Research Centre, Cork, Ireland
- Dairy Processing Technology Centre (DPTC), Limerick, Ireland
| | - Mark A. Fenelon
- Teagasc Food Research Centre, Cork, Ireland
- VistaMilk SFI Research Centre, Cork, Ireland
- Dairy Processing Technology Centre (DPTC), Limerick, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
- VistaMilk SFI Research Centre, Cork, Ireland
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24
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Wysok B, Rudowska M, Wiszniewska-Łaszczych A. The Transmission of Campylobacter Strains in Dairy Herds in Different Housing Systems. Pathogens 2024; 13:317. [PMID: 38668272 PMCID: PMC11053475 DOI: 10.3390/pathogens13040317] [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: 03/08/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/29/2024] Open
Abstract
Cattle are frequent carriers of Campylobacter spp.; therefore, these bacteria may be transmitted to humans through meat or milk. Campylobacter spp. in raw milk derives most commonly from secondary fecal contamination during the milking process; however, the udder excretion of Campylobacter may be a cause of milk-borne infection. Studies were carried out on a Campylobacter-positive farm with two different housing systems (with free-stall and tie-stall systems). The sampling process comprised several stages, including samples being taken from animals, such as from raw milk and feces, and from the environment, such as the from floor in the milking parlor and from teat cups. None of the individual raw milk samples or swabs from the floor in the parlor before the milking process were positive for Campylobacter spp. Simultaneously, Campylobacter spp. was isolated from all swabs from the floor after the milking process and in the bulk tank milk samples from the two farms. The incidence of Campylobacter isolated from fecal and teat swab samples ranged from 15.4% to 26.7% and from 8.9% to 25%, respectively. Altogether, 59 recovered Campylobacter isolates were classified, based on sequencing of the flaA short variable region, showing 15 different allele types, and the majority of them were distributed among one farm. Analysis of the virulence and antimicrobial properties showed that genes related to adherence, invasion and cytotoxicity were widely distributed among the Campylobacter recovered strains. In relation to AMR, multidrug resistance was noted in 16.1% of strains.
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Affiliation(s)
- Beata Wysok
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Oczapowskiego 14, 10-718 Olsztyn, Poland
| | - Małgorzata Rudowska
- Department of Animal Reproduction with Clinic, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Oczapowskiego 14, 10-718 Olsztyn, Poland
| | - Agnieszka Wiszniewska-Łaszczych
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Oczapowskiego 14, 10-718 Olsztyn, Poland
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25
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Somrup S, Mitsuwan W, Bhumibhamon T, Pereira MDL, Paul AK, Nissapatorn V, Saengsawang P. Antibiograms, multidrug resistance, and milk-related parameters of bacteria isolated from milk of dairy cattle in Phatthalung, Thailand. Vet World 2024; 17:735-743. [PMID: 38798280 PMCID: PMC11111717 DOI: 10.14202/vetworld.2024.735-743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/01/2024] [Indexed: 05/29/2024] Open
Abstract
Background and Aim Milk, a nutritious food, is widely consumed in human diets; however, contamination by micro-organisms can negatively impact its quality and consumer health. Contamination by micro-organisms affects the quality of milk, which can affect the quality of the milk production chain. This study aimed to determine the changes in milk composition and antibiotic susceptibility related to bacteria isolated from dairy cow milk. Materials and Methods Raw milk samples were collected from 72 dairy cows. All milk samples were subjected to the California Mastitis Test (CMT) for CMT score determination. We also investigated milk composition, bacterial culture (BC), and antibiotic susceptibility. Results About 47.22% and 30.56% of dairy cattle were positive for CMT + BC and automatic somatic cell count (ASCC) + BC, respectively. Fecal appearance and animal age were found to be risk factors for ASCC + BC positivity in dairy cattle. Bacteria were found in approximately 76% of milk samples, with the most common isolated species being α-hemolytic Streptococcus spp., coagulase-negative Staphylococcus spp., and Escherichia coli. Of these, 70% are resistant to at least one antibiotic. Variation in the multidrug resistance pattern was high in Klebsiella spp. Conclusions Fecal appearance and animal age are risk factors for ASCC + BC positivity in dairy cattle. This study identified antibiotic and multidrug resistance patterns, which require comprehensive studies and effective surveillance systems. Remarkably, the use of antibiotic therapy in dairy cattle should be monitored.
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Affiliation(s)
- Supaporn Somrup
- Faculty of Technology and Community Development, Thaksin University, Phatthalung 93210, Thailand
| | - Watcharapong Mitsuwan
- Akkhraratchakumari Veterinary College, Walailak University, Nakhon Si Thammarat 80160, Thailand
- One Health Research Center, Walailak University, Nakhon Si Thammarat 80160, Thailand
- Center of Excellence in Innovation of Essential Oils, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Teeraphun Bhumibhamon
- Veterinary Research and Development Center (Upper Southern Region), Nakhon Si Thammarat 80110, Thailand
| | - Maria de Lourdes Pereira
- Department of Medical Sciences, CICECO-Aveiro Institute of Materials, University of Aveiro, Aveiro 3810-193, Portugal
| | - Alok K. Paul
- School of Pharmacy and Pharmacology, University of Tasmania, Hobart, Australia
| | - Veeranoot Nissapatorn
- School of Allied Health Sciences, Southeast Asia Water Team, World Union for Herbal Drug Discovery, and Research Excellence Center for Innovation and Health Products, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Phirabhat Saengsawang
- Akkhraratchakumari Veterinary College, Walailak University, Nakhon Si Thammarat 80160, Thailand
- One Health Research Center, Walailak University, Nakhon Si Thammarat 80160, Thailand
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26
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Yasir M, Al-Zahrani IA, Khan R, Soliman SA, Turkistani SA, Alawi M, Azhar EI. Microbiological risk assessment and resistome analysis from shotgun metagenomics of bovine colostrum microbiome. Saudi J Biol Sci 2024; 31:103957. [PMID: 38404539 PMCID: PMC10891335 DOI: 10.1016/j.sjbs.2024.103957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/05/2024] [Accepted: 02/10/2024] [Indexed: 02/27/2024] Open
Abstract
Colostrum is known for its nutraceutical qualities, probiotic attributes, and health benefits. The aim of this study was to profile colostrum microbiome from bovine in rural sites of a developing country. The focus was on microbiological safety assessments and antimicrobial resistance, taking into account the risks linked with the consumption of raw colostrum. Shotgun sequencing was employed to analyze microbiome in raw buffalo and cow colostrum. Alpha and beta diversity analyses revealed increased inter and intra-variability within colostrum samples' microbiome from both livestock species. The colostrum microbiome was mainly comprised of bacteria, with over 90% abundance, whereas fungi and viruses were found in minor abundance. Known probiotic species, such as Leuconostoc mesenteroides, Lactococcus lactis, Streptococcus thermophilus, and Lactobacillus paracasei, were found in the colostrum samples. A relatively higher number of pathogenic and opportunistic pathogenic bacteria were identified in colostrum from both animals, including clinically significant bacteria like Clostridium botulinum, Pseudomonas aeruginosa, Escherichia coli, and Listeria monocytogenes. Binning retrieved 11 high-quality metagenome-assembled genomes (MAGs), with three MAGs potentially representing novel species from the genera Psychrobacter and Pantoea. Notably, 175 antimicrobial resistance genes (ARGs) and variants were detected, with 55 of them common to both buffalo and cow colostrum metagenomes. These ARGs confer resistance against aminoglycoside, fluoroquinolone, tetracycline, sulfonamide, and peptide antibiotics. In conclusion, this study describes a thorough overview of microbial communities in buffalo and cow colostrum samples. It emphasizes the importance of hygienic processing and pasteurization in minimizing the potential transmission of harmful microorganisms linked to the consumption of colostrum.
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Affiliation(s)
- Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ibrahim A. Al-Zahrani
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Raees Khan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | | | - Safaa A. Turkistani
- Medical Laboratory Sciences, Fakeeh College for Medical Sciences, Jeddah 21134, Saudi Arabia
| | - Maha Alawi
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Infection Control & Environmental Health Unit, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Esam I. Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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27
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Gensler CA, Hempstead SC, Keelara S, Fedorka-Cray PJ, Urie NJ, Wiedenheft AM, Stuart K, Marshall KL, Jacob ME. Antimicrobial Resistance Characteristics of Fecal Escherichia coli and Enterococcus Species in U.S. Goats: 2019 National Animal Health Monitoring System Enteric Study. Foodborne Pathog Dis 2024. [PMID: 38502797 DOI: 10.1089/fpd.2023.0089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024] Open
Abstract
Escherichia coli and Enterococcus species are normal bacteria of the gastrointestinal tract and serve as indicator organisms for the epidemiology and emergence of antimicrobial resistance in their hosts and the environment. Some E. coli serovars, including E. coli O157:H7, are important human pathogens, although reservoir species such as goats remain asymptomatic. We describe the prevalence and antimicrobial resistance of generic E. coli, E. coli O157:H7, and Enterococcus species collected from a national surveillance study of goat feces as part of the National Animal Health Monitoring System (NAHMS) Goat 2019 study. Fecal samples were collected from 4918 goats on 332 operations across the United States. Expectedly, a high prevalence of E. coli (98.7%, 4850/4915) and Enterococcus species (94.8%, 4662/4918) was found. E. coli O157:H7 prevalence was low (0.2%; 10/4918). E. coli isolates, up to three per operation, were evaluated for antimicrobial susceptibility and 84.7% (571/674) were pansusceptible. Multidrug resistance (MDR; ≥3 classes) was uncommon among E. coli, occurring in 8.2% of isolates (55/674). Resistance toward seven antimicrobial classes was observed in a single isolate. Resistance to tetracycline alone (13.6%, 92/674) or to tetracycline, streptomycin, and sulfisoxazole (7.0% 47/674) was the most common pattern. All E. coli O157:H7 isolates were pansusceptible. Enterococcus isolates, up to four per operation, were prioritized by public health importance, including Enterococcus faecium and Enterococcus faecalis and evaluated. Resistance to lincomycin (93.8%, 1232/1313) was most common, with MDR detected in 29.5% (388/1313) of isolates. The combination of ciprofloxacin, lincomycin, and quinupristin resistance (27.1%, 105/388) was the most common pattern detected. Distribution and characteristics of antimicrobial resistance in E. coli and Enterococcus in the U.S. goat population from this study can inform stewardship considerations and public health efforts surrounding goats and their products.
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Affiliation(s)
- Catherine A Gensler
- Department of Agricultural and Human Sciences, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Stephanie C Hempstead
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Shivaramu Keelara
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Paula J Fedorka-Cray
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Natalie J Urie
- National Animal Health Monitoring System, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, Colorado, USA
| | - Alyson M Wiedenheft
- National Animal Health Monitoring System, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, Colorado, USA
- Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Keira Stuart
- National Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, Iowa, USA
| | - Katherine L Marshall
- National Animal Health Monitoring System, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, Colorado, USA
| | - Megan E Jacob
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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28
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Czeszewska-Rosiak G, Złoch M, Radosińska M, Florkiewicz AB, Tretyn A, Pomastowski P. The usefulness of the MALDI-TOF MS technique in the determination of dairy samples' microbial composition: comparison of the new EXS 2600 system with MALDI Biotyper platform. Arch Microbiol 2024; 206:172. [PMID: 38492038 DOI: 10.1007/s00203-024-03885-w] [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: 11/30/2023] [Revised: 01/15/2024] [Accepted: 02/05/2024] [Indexed: 03/18/2024]
Abstract
This study compared the EXS 2600 system with the MALDI Biotyper for identifying microorganisms in dairy samples. Of the 196 bacterial isolates from milk, whey, buttermilk, cream, and dairy wastewater, the species and genus consistent identification between two systems showed 74% and 99%, respectively. However, the level of species identification rate exhibited a difference, which was higher in Zybio than in Bruker-76.0% and 66.8%, respectively. Notably, the EXS 2600 system performed better with certain yeast species and H. alvei, while the Biotyper excelled with Pseudomonas bacteria. Unique microbial compositions were found in 85% of dairy samples, with whey and buttermilk having the highest diversity. This research highlights the EXS 2600's potential as a reliable dairy microbial identification tool and underscores the need for a more diverse and comprehensive spectral database, despite the database's focus on clinical applications (as announced).
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Affiliation(s)
- Grażyna Czeszewska-Rosiak
- Chair of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Lwowska 1 Street, 87-100, Toruń, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4 Str., 87-100, Toruń, Poland
| | - Michał Złoch
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4 Str., 87-100, Toruń, Poland.
| | - Monika Radosińska
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4 Str., 87-100, Toruń, Poland
| | | | - Andrzej Tretyn
- Chair of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Lwowska 1 Street, 87-100, Toruń, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4 Str., 87-100, Toruń, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4 Str., 87-100, Toruń, Poland
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Sun M, Shao W, Liu Z, Ma X, Chen H, Zheng N, Zhao Y. Microbial diversity in camel milk from Xinjiang, China as revealed by metataxonomic analysis. Front Microbiol 2024; 15:1367116. [PMID: 38533337 PMCID: PMC10964795 DOI: 10.3389/fmicb.2024.1367116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
The quality of raw camel milk is affected by its bacterial composition and diversity. However, few studies have investigated the bacterial composition and diversity of raw camel milk. In this study, we obtained 20 samples of camel milk during spring and summer in Urumqi and Hami, Xinjiang, China. Single-molecule real-time sequencing technology was used to analyze the bacterial community composition. The results revealed that there were significant seasonal differences in the bacterial composition and diversity of camel milk. Overall, Epilithonimonas was the most abundant bacterial genus in our samples. Through the annotated genes inferred by PICRUSt2 were mapped against KEGG database. Non-parametric analysis of the bacterial community prediction function revealed a strong bacterial interdependence with metabolic pathways (81.83%). There were clear regional and seasonal differences in level 3 metabolic pathways such as fat, vitamins, and amino acids in camel milk. In addition, we identified lactic acid bacteria in camel milk with antibacterial and anti-tumor activities. Our findings revealed that camel milk from Xinjiang had serious risk of contamination by psychrophilic and pathogenic bacteria. Our research established a crucial theoretical foundation for ensuring the quality and safety of camel milk, thereby contributing significantly to the robust growth of China's camel milk industry.
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Affiliation(s)
- Miao Sun
- Institute of Quality Standards and Testing Technology for Agro-Products, Xinjiang Academy of Agricultural Sciences, Laboratory of Quality and Safety Risk Assessment for Agro-products, Ministry of Agriculture, Urumqi, China
- College of Animal Science Xinjiang Agriculture University, Urumqi, China
| | - Wei Shao
- College of Animal Science Xinjiang Agriculture University, Urumqi, China
| | - Zhengyu Liu
- Institute of Quality Standards and Testing Technology for Agro-Products, Xinjiang Academy of Agricultural Sciences, Laboratory of Quality and Safety Risk Assessment for Agro-products, Ministry of Agriculture, Urumqi, China
- College of Animal Science Xinjiang Agriculture University, Urumqi, China
| | - Xianlan Ma
- Institute of Quality Standards and Testing Technology for Agro-Products, Xinjiang Academy of Agricultural Sciences, Laboratory of Quality and Safety Risk Assessment for Agro-products, Ministry of Agriculture, Urumqi, China
| | - He Chen
- Institute of Quality Standards and Testing Technology for Agro-Products, Xinjiang Academy of Agricultural Sciences, Laboratory of Quality and Safety Risk Assessment for Agro-products, Ministry of Agriculture, Urumqi, China
| | - Nan Zheng
- Ministry of Agriculture Laboratory of Quality and Safety Risk Assessment for Dairy Products, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yankun Zhao
- Institute of Quality Standards and Testing Technology for Agro-Products, Xinjiang Academy of Agricultural Sciences, Laboratory of Quality and Safety Risk Assessment for Agro-products, Ministry of Agriculture, Urumqi, China
- Ministry of Agriculture Laboratory of Quality and Safety Risk Assessment for Dairy Products, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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30
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Huuki H, Vilkki J, Vanhatalo A, Tapio I. Fecal microbiota colonization dynamics in dairy heifers associated with early-life rumen microbiota modulation and gut health. Front Microbiol 2024; 15:1353874. [PMID: 38505558 PMCID: PMC10949896 DOI: 10.3389/fmicb.2024.1353874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/07/2024] [Indexed: 03/21/2024] Open
Abstract
Early-life modulation of rumen microbiota holds promise for enhancing calf growth, health, and long-term production in ruminants. However, limited attention has been given to the impact of rumen microbiota modulation on the establishment of hindgut microbiota. In this study, fecal microbiota development was examined in identical twin calves for 12 months. The treatment group (T-group) received adult cow fresh rumen liquid inoculum during the pre-weaning period, while the control group did not (C-group). The effects of inoculum were assessed on calf gut health and as microbial seeding route into the hindgut. The early rumen modulation had no effect on age-related fecal microbiota development. The fecal bacterial community evolved gradually following dietary changes and categorized into pre-weaning and post-weaning communities. Bacterial richness increased with age and stabilized at month 9, while between-sample variation reduced in post-weaning samples. Archaeal load in fecal samples increased after month 4, while archaeal richness increased and stabilized in both groups by month 9. Between-sample similarity was higher during the pre-weaning period, with increased dissimilarity from month 4 onward. Anaerobic fungi were detected in feces at month 4, with richness peaking at month 7. Before month 6, fungal community composition distinctly differed from mature communities. When colostrum, calf rumen, and donor inoculum were evaluated as seeding sources for hindgut colonization, the calf's own rumen was identified as the primary seeding source for fecal bacteria and fungi. Colostrum was a source for several bacteria detected in feces, but these were of temporary importance until weaning. The donor inoculum had limited impact on gut health as diarrhea rates were similar between the T-group and C-group. In conclusion, early-life microbiota modulation shows potential in ruminant development. However, a more targeted approach with bacteria adapted to the hindgut environment may be necessary to modulate hindgut effectively. This research contributes to our understanding of the complex relationship between gut microbiota and calf health and growth.
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Affiliation(s)
- Hanna Huuki
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- Production Systems, Genomics and Breeding, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Johanna Vilkki
- Production Systems, Genomics and Breeding, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Aila Vanhatalo
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Ilma Tapio
- Production Systems, Genomics and Breeding, Natural Resources Institute Finland (Luke), Jokioinen, Finland
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Decadt H, Weckx S, De Vuyst L. The microbial and metabolite composition of Gouda cheese made from pasteurized milk is determined by the processing chain. Int J Food Microbiol 2024; 412:110557. [PMID: 38237418 DOI: 10.1016/j.ijfoodmicro.2024.110557] [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: 08/17/2023] [Revised: 12/26/2023] [Accepted: 01/01/2024] [Indexed: 01/28/2024]
Abstract
Gouda cheeses of different production batches and ripening times often differ in metabolite composition, which may be due to the starter culture mixture applied or the growth of non-starter lactic acid bacteria (NSLAB) upon maturation. Therefore, a single Gouda cheese production batch was systematically investigated from the thermized milk to the mature cheeses, ripened for up to 100 weeks, to identify the main bacterial species and metabolites and their dynamics during the whole production and ripening. As this seemed to be starter culture strain- and NSLAB-dependent, it requested a detailed, longitudinal, and quantitative investigation. Hereto, microbial colony enumeration, high-throughput full-length 16S rRNA gene sequencing, and a metabolomic approach were combined. Culture-dependently, Lactococcus lactis was the most abundant species from its addition as part of the starter culture up to the first two months of cheese ripening. Afterward, the NSLAB Lacticaseibacillus paracasei became the main species during ripening. The milk was a possible inoculation source for the latter species, despite pasteurization. Culture-independently, the starter LAB Lactococcus cremoris and Lc. lactis were the most abundant species in the cheese core throughout the whole fermentation and ripening phases up to 100 weeks. The cheese rind from 40 until 100 weeks of ripening was characterized by a high relative abundance of the NSLAB Tetragenococcus halophilus and Loigolactobacillus rennini, which both came from the brine. These species were linked with the production of the biogenic amines cadaverine and putrescine. The most abundant volatile organic compound was acetoin, an indicator of citrate and lactose fermentation during the production day, whereas the concentrations of free amino acids were an indicator of the ripening time.
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Affiliation(s)
- Hannes Decadt
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
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32
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Martuzzi F, Franceschi P, Formaggioni P. Fermented Mare Milk and Its Microorganisms for Human Consumption and Health. Foods 2024; 13:493. [PMID: 38338628 PMCID: PMC10855475 DOI: 10.3390/foods13030493] [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: 12/22/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
Mare milk is consumed by approximatively 30 million people in the world. In countries in Asia and East Europe, mare milk is mainly consumed as source of fermented products, called koumiss, airag or chigee, alcoholic beverages obtained by means of a culture of bacteria and lactose-fermenting yeasts. Recent research concerning mare milk and its derivatives deals mainly with their potential employment for human health. Studies about the isolation and characterization of Lactobacillus spp. and yeasts from koumiss have been aimed at assessing the potential functional properties of these micro-organisms and to find their employment for the industrial processing of mare milk. The aim of this literature review is to summarize recent research about microorganisms in fermented mare milk products and their potential functional properties.
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Affiliation(s)
- Francesca Martuzzi
- Department of Food and Drug Science, University of Parma, Via delle Scienze, 43124 Parma, Italy;
| | - Piero Franceschi
- Department of Veterinary Science, University of Parma, Via del Taglio 10, 43126 Parma, Italy;
| | - Paolo Formaggioni
- Department of Veterinary Science, University of Parma, Via del Taglio 10, 43126 Parma, Italy;
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33
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Galli BD, Nikoloudaki O, Granehäll L, Carafa I, Pozza M, De Marchi M, Gobbetti M, Di Cagno R. Comparative analysis of microbial succession and proteolysis focusing on amino acid pathways in Asiago-PDO cheese from two dairies. Int J Food Microbiol 2024; 411:110548. [PMID: 38154252 DOI: 10.1016/j.ijfoodmicro.2023.110548] [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: 08/07/2023] [Revised: 11/18/2023] [Accepted: 12/17/2023] [Indexed: 12/30/2023]
Abstract
In this study, a comprehensive and comparative analysis was conducted on Italian Asiago-PDO cheese obtained from two different dairies named Dairy I and Dairy II using industrial and natural fermented milk, respectively. The analysis encompassed the evaluation of chemical composition, the succession of the microbiota during manufacture and ripening, and proteolysis mainly focusing on free individual amino acid (FAA) profiles. A metagenomic approach was used to investigate the cheese microbiome functionality. Differences in gross chemical composition were more evident during ripening, with Dairy II showing higher variability within batches. The microbiota varied significantly between the two dairies and ripening stages. The choice of starter culture shaped the microbiota during production and affected the microbial diversity of non-starter lactic acid bacteria (NSLAB) originated from the raw milk during ripening. Peptide chromatographic profiles and FAA concentrations increased as ripening progressed, with Dairy I showing higher production of FAA. Functional analysis of the metagenomes linked species to specific amino acid metabolism/catabolism pathways. The amino acid metabolism pathways, particularly those related to aromatic amino acids, lysine, and branched-chain amino acids, were affected by the presence of specific NSLAB species, which differed between the two dairies. The results obtained in this study reveal the impact of starter culture on peculiar cheese microbiota assemblies, which selectively targets amino acid pathways, providing insights into the potential flavor and aroma characteristics of Asiago-PDO cheese.
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Affiliation(s)
- Bruno Domingues Galli
- Free University of Bozen-Bolzano, Faculty of Agricultural, Environmental and Food Sciences, Piazza Università 1, 39100 Bolzano, BZ, Italy
| | - Olga Nikoloudaki
- Free University of Bozen-Bolzano, Faculty of Agricultural, Environmental and Food Sciences, Piazza Università 1, 39100 Bolzano, BZ, Italy.
| | - Lena Granehäll
- Free University of Bozen-Bolzano, Faculty of Agricultural, Environmental and Food Sciences, Piazza Università 1, 39100 Bolzano, BZ, Italy.
| | - Ilaria Carafa
- Free University of Bozen-Bolzano, Faculty of Agricultural, Environmental and Food Sciences, Piazza Università 1, 39100 Bolzano, BZ, Italy
| | - Marta Pozza
- University of Padova, Department of Agronomy, Food, Natural resources, Animals and Environment, Viale dell'Università 16, 35020 Legnaro, PD, Italy.
| | - Massimo De Marchi
- University of Padova, Department of Agronomy, Food, Natural resources, Animals and Environment, Viale dell'Università 16, 35020 Legnaro, PD, Italy.
| | - Marco Gobbetti
- Free University of Bozen-Bolzano, Faculty of Agricultural, Environmental and Food Sciences, Piazza Università 1, 39100 Bolzano, BZ, Italy.
| | - Raffaella Di Cagno
- Free University of Bozen-Bolzano, Faculty of Agricultural, Environmental and Food Sciences, Piazza Università 1, 39100 Bolzano, BZ, Italy.
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Lan X, Wu S, Du Q, Min L. The Investigation of Changes in Bacterial Community of Pasteurized Milk during Cold Storage. Foods 2024; 13:451. [PMID: 38338585 PMCID: PMC10855270 DOI: 10.3390/foods13030451] [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: 11/09/2023] [Revised: 12/25/2023] [Accepted: 12/30/2023] [Indexed: 02/12/2024] Open
Abstract
The quality of pasteurized milk is commonly assessed through microbiological analysis, with variations in storage conditions significantly impacting the suppression of bacterial growth throughout the milk's shelf life. This study investigated the dynamics of total bacterial counts (TBCs) and bacterial community shifts in milk that underwent pasteurization at 80 °C for 15 s. The milk was subsequently stored at 4 °C for varying intervals of 1, 4, 7, 10, 13, and 16 days. Culture-based testing revealed a significant TBC increase during the storage period spanning 1 to 16 days (up to -log10 4.2 CFU/mL at day 16). The TBC in pasteurized milk exhibited accelerated microbial growth from day 13 onwards, ultimately peaking on day 16. Bacillus was detected through 16S rRNA identification. Principal component analysis demonstrated a significant impact of storage time on bacterial communities in pasteurized milk. Analysis of bacterial diversity revealed a negative correlation between the Shannon index and the duration of pasteurized milk storage. Using high-throughput sequencing, Streptococcus and Acinetobacter were detected as prevalent bacterial genera, with Streptococcus dysgalactiae and Streptococcus uberis showing as dominant taxa. The presence of Streptococcus dysgalactiae and Streptococcus uberis in pasteurized milk might be attributed to the initial contamination from raw milk with mastitis. This study offers new evidence of the prevalence of bacterial community in pasteurized milk, thereby adding value to the enhancement of quality control and the development of strategies for reducing microbial risks.
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Affiliation(s)
- Xinyi Lan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China;
| | - Shuyan Wu
- Hopkirk Research Institute, AgResearch Ltd., Palmerston North 4442, New Zealand;
| | - Qijing Du
- Grasslands Research Centre, AgResearch Ltd., Palmerston North 4472, New Zealand;
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Li Min
- Ministry of Agriculture Key Laboratory of Animal Nutrition and Feed Science in South China, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
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35
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Sionek B, Okoń A, Łepecka A, Zielińska D, Jaworska D, Kajak-Siemaszko K, Neffe-Skocińska K, Trząskowska M, Karbowiak M, Szymański P, Dolatowski ZJ, Kołożyn-Krajewska D. The Role of Autochthonous Levilactobacillus brevis B1 Starter Culture in Improving the Technological and Nutritional Quality of Cow's Milk Acid-Rennet Cheeses-Industrial Model Study. Foods 2024; 13:392. [PMID: 38338527 PMCID: PMC10855195 DOI: 10.3390/foods13030392] [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: 12/21/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
In the study, an attempt was made to develop an innovative technology for cheese manufacturing. It was hypothesized that selected autochthonous lactic acid bacteria as a starter culture are more suitable for the production of acid-rennet cheeses of good technological and sensory quality. The study aimed to assess the possibility of using the strain Levilactobacillus brevis B1 (L. brevis B1) as a starter culture to produce acid-rennet cheeses using raw cow's milk. Two variants of cheese were manufactured. The control variant (R) was coagulated with microbial rennet and buttermilk, and the other variant (B1) was inoculated with rennet and L. brevis B1 starter culture. The effect of the addition of these autochthonous lactic acid bacteria on selected physicochemical characteristics, durability, the composition of fatty acids, cholesterol, Iipid Quality Indices, and microbiological and sensory quality of acid-rennet cheeses was determined during a 3-month period of storage. The dominant fatty acids observed in the tested cheeses were saturated fatty acids (SFA) (68.43-69.70%) and monounsaturated fatty acids (MUFA) (25.85-26.55%). Significantly higher polyunsaturated fatty acid (PUFA) content during storage was observed for B1 cheeses. The B1 cheeses were characterized by lower cholesterol content compared to cheese R and showed better indexes, including the Index of atherogenicity, Index of thrombogenicity, DFA, OFA, H/H, and HPI indexes, than the R cheese. No effect of the tested L. brevis B1 on sensory quality was observed in relation to the control cheeses during 3 months of storage. The results of the research indicate the possibility of using the L. brevis B1 strain for the production of high-quality, potentially probiotic acid-rennet cheeses.
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Affiliation(s)
- Barbara Sionek
- Department of Food Gastronomy and Food Hygiene, Institute of Human Nutrition Sciences, Warsaw University of Life Sciences (SGGW), 02-776 Warsaw, Poland; (D.Z.); (D.J.); (K.K.-S.); (K.N.-S.); (M.T.); (M.K.); (D.K.-K.)
| | - Anna Okoń
- Department of Meat and Fat Technology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, 36 Rakowiecka St, 02-532 Warsaw, Poland; (A.O.); (A.Ł.); (P.S.); (Z.J.D.)
| | - Anna Łepecka
- Department of Meat and Fat Technology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, 36 Rakowiecka St, 02-532 Warsaw, Poland; (A.O.); (A.Ł.); (P.S.); (Z.J.D.)
| | - Dorota Zielińska
- Department of Food Gastronomy and Food Hygiene, Institute of Human Nutrition Sciences, Warsaw University of Life Sciences (SGGW), 02-776 Warsaw, Poland; (D.Z.); (D.J.); (K.K.-S.); (K.N.-S.); (M.T.); (M.K.); (D.K.-K.)
| | - Danuta Jaworska
- Department of Food Gastronomy and Food Hygiene, Institute of Human Nutrition Sciences, Warsaw University of Life Sciences (SGGW), 02-776 Warsaw, Poland; (D.Z.); (D.J.); (K.K.-S.); (K.N.-S.); (M.T.); (M.K.); (D.K.-K.)
| | - Katarzyna Kajak-Siemaszko
- Department of Food Gastronomy and Food Hygiene, Institute of Human Nutrition Sciences, Warsaw University of Life Sciences (SGGW), 02-776 Warsaw, Poland; (D.Z.); (D.J.); (K.K.-S.); (K.N.-S.); (M.T.); (M.K.); (D.K.-K.)
| | - Katarzyna Neffe-Skocińska
- Department of Food Gastronomy and Food Hygiene, Institute of Human Nutrition Sciences, Warsaw University of Life Sciences (SGGW), 02-776 Warsaw, Poland; (D.Z.); (D.J.); (K.K.-S.); (K.N.-S.); (M.T.); (M.K.); (D.K.-K.)
| | - Monika Trząskowska
- Department of Food Gastronomy and Food Hygiene, Institute of Human Nutrition Sciences, Warsaw University of Life Sciences (SGGW), 02-776 Warsaw, Poland; (D.Z.); (D.J.); (K.K.-S.); (K.N.-S.); (M.T.); (M.K.); (D.K.-K.)
| | - Marcelina Karbowiak
- Department of Food Gastronomy and Food Hygiene, Institute of Human Nutrition Sciences, Warsaw University of Life Sciences (SGGW), 02-776 Warsaw, Poland; (D.Z.); (D.J.); (K.K.-S.); (K.N.-S.); (M.T.); (M.K.); (D.K.-K.)
| | - Piotr Szymański
- Department of Meat and Fat Technology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, 36 Rakowiecka St, 02-532 Warsaw, Poland; (A.O.); (A.Ł.); (P.S.); (Z.J.D.)
| | - Zbigniew J. Dolatowski
- Department of Meat and Fat Technology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, 36 Rakowiecka St, 02-532 Warsaw, Poland; (A.O.); (A.Ł.); (P.S.); (Z.J.D.)
| | - Danuta Kołożyn-Krajewska
- Department of Food Gastronomy and Food Hygiene, Institute of Human Nutrition Sciences, Warsaw University of Life Sciences (SGGW), 02-776 Warsaw, Poland; (D.Z.); (D.J.); (K.K.-S.); (K.N.-S.); (M.T.); (M.K.); (D.K.-K.)
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36
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Ritschard JS, Schuppler M. The Microbial Diversity on the Surface of Smear-Ripened Cheeses and Its Impact on Cheese Quality and Safety. Foods 2024; 13:214. [PMID: 38254515 PMCID: PMC10814198 DOI: 10.3390/foods13020214] [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: 12/07/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Smear-ripened cheeses are characterized by a viscous, red-orange surface smear on their rind. It is the complex surface microbiota on the cheese rind that is responsible for the characteristic appearance of this cheese type, but also for the wide range of flavors and textures of the many varieties of smear-ripened cheeses. The surface smear microbiota also represents an important line of defense against the colonization with undesirable microorganisms through various types of interaction, such as competitive exclusion or production of antimicrobial substances. Predominant members of the surface smear microbiota are salt-tolerant yeast and bacteria of the phyla Actinobacteria, Firmicutes, and Proteobacteria. In the past, classical culture-based approaches already shed light on the composition and succession of microorganisms and their individual contribution to the typicity of this cheese type. However, during the last decade, the introduction and application of novel molecular approaches with high-resolution power provided further in-depth analysis and, thus, a much more detailed view of the composition, structure, and diversity of the cheese smear microbiota. This led to abundant novel knowledge, such as the identification of so far unknown community members. Hence, this review is summarizing the current knowledge of the diversity of the surface smear microbiota and its contribution to the quality and safety of smear-ripened cheese. If the succession or composition of the surface-smear microbiota is disturbed, cheese smear defects might occur, which may promote food safety issues. Hence, the discussion of cheese smear defects in the context of an increased understanding of the intricate surface smear ecosystem in this review may not only help in troubleshooting and quality control but also paves the way for innovations that can lead to safer, more consistent, and higher-quality smear-ripened cheeses.
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Affiliation(s)
| | - Markus Schuppler
- Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland;
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Elcheninov AG, Zayulina KS, Klyukina AA, Kremneva MK, Kublanov IV, Kochetkova TV. Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia. Microorganisms 2023; 12:16. [PMID: 38276185 PMCID: PMC10819033 DOI: 10.3390/microorganisms12010016] [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: 11/18/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Fermented milk products (FMPs) contain probiotics that are live bacteria considered to be beneficial to human health due to the production of various bioactive molecules. In this study, nine artisanal FMPs (kefir, ayran, khurunga, shubat, two cottage cheeses, bryndza, khuruud and suluguni-like cheese) from different regions of Russia were characterized using metagenomics. A metagenomic sequencing of ayran, khurunga, shubat, khuruud and suluguni-like cheese was performed for the first time. The taxonomic profiling of metagenomic reads revealed that Lactococcus species, such as Lc. lactis and Lc. cremoris prevailed in khuruud, bryndza, one sample of cottage cheese and khurunga. The latter one together with suluguni-like cheese microbiome was dominated by bacteria, affiliated to Lactobacillus helveticus (32-35%). In addition, a high proportion of sequences belonging to the genera Lactobacillus, Lactococcus and Streptococcus but not classified at the species level were found in the suluguni-like cheese. Lactobacillus delbrueckii, as well as Streptococcus thermophilus constituted the majority in another cottage cheese, kefir and ayran metagenomes. The microbiome of shubat, produced from camel's milk, was significantly distinctive, and Lentilactobacillus kefiri, Lactobacillus kefiranofaciens and Bifidobacterium mongoliense represented the dominant components (42, 7.4 and 5.6%, respectively). In total, 78 metagenome-assembled genomes with a completeness ≥ 50.2% and a contamination ≤ 8.5% were recovered: 61 genomes were assigned to the Enterococcaceae, Lactobacillaceae and Streptococcaceae families (the Lactobacillales order within Firmicutes), 4 to Bifidobacteriaceae (the Actinobacteriota phylum) and 2 to Acetobacteraceae (the Proteobacteria phylum). A metagenomic analysis revealed numerous genes, from 161 to 1301 in different products, encoding glycoside hydrolases and glycosyltransferases predicted to participate in lactose, alpha-glucans and peptidoglycan hydrolysis as well as exopolysaccharides synthesis. A large number of secondary metabolite biosynthetic gene clusters, such as lanthipeptides, unclassified bacteriocins, nonribosomal peptides and polyketide synthases were also detected. Finally, the genes involved in the synthesis of bioactive compounds like β-lactones, terpenes and furans, nontypical for fermented milk products, were also found. The metagenomes of kefir, ayran and shubat was shown to contain either no or a very low count of antibiotic resistance genes. Altogether, our results show that traditional indigenous fermented products are a promising source of novel probiotic bacteria with beneficial properties for medical and food industries.
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Affiliation(s)
- Alexander G. Elcheninov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
| | - Kseniya S. Zayulina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
| | - Alexandra A. Klyukina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
| | - Mariia K. Kremneva
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia;
| | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
| | - Tatiana V. Kochetkova
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
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Sioziou E, Kakouri A, Bosnea L, Samelis J. Antilisterial activity of raw sheep milk from two native Epirus breeds: Culture-dependent identification, bacteriocin gene detection and primary safety evaluation of the antagonistic LAB biota. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 6:100209. [PMID: 38116185 PMCID: PMC10727937 DOI: 10.1016/j.crmicr.2023.100209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023] Open
Abstract
Raw milk from native small ruminant breeds in Epirus, Greece, is a valuable natural source of autochthonous lactic acid bacteria (LAB) strains with superior biotechnological properties. In this study, two bulk milks (RM1, RM2) from two local sheep yards, intended for traditional Kefalotyri cheese production, were preselected for bacteriocin-like antilisterial activity by in vitro tests. Their antagonistic LAB biota was quantified followed by polyphasic (16S rRNA gene sequencing; IGS for Enterococcus; a multiplex-PCR for Leuconostoc) identification of 42 LAB (RM1/18; RM2/24) isolates further evaluated for bacteriocin encoding genes and primary safety traits. Representative isolates of the numerically dominant mesophilic LAB were Leuconostoc mesenteroides (10) in both RMs, Streptococcus parauberis (7) in RM2, and Lactococcus lactis (1) in RM1; the subdominant thermophilic LAB isolates were Enterococcus durans (8), E. faecium (6), E. faecalis (3), E. hirae (1), E. hermanniensis (1), Streptococcus lutetiensis (2), S. equinus (1) and S. gallolyticus (1). Based on their rpoB, araA, dsr and sorA profiles, six Ln. mesenteroides strains (8 isolates) were atypical lying between the subspecies mesenteroides and dextranicum, whereas two strains profiled with Ln. mesenteroides subsp. jonggajibkimchi that is first-time reported in Greek dairy food. Two RM1 E. faecium strain biotypes (3 isolates) showed strong, enterocin-mediated antilisterial activity due to entA/entB/entP possession. One E. durans from RM1 possessed entA and entP, while additional nine RM2 isolates of the E. faecium/durans group processed entA or entP singly. All showed direct (cell-associated) antilisterial activity only, as also both S. lutetiensis strains from RM2 did strongly. Desirably, no LAB isolate was β-hemolyrtic, or cytolysin-positive, or possessed vanA, vanB for vancomycin resistance, or agg, espA, hyl, and IS16 virulence genes. However, all three E. faecalis from RM2 possessed gelE and/or ace virulence genes. In conclusion, all Ln. mesenteroides strains, the two safe, enterocin A-B-P-producing E. faecium strains, and the two antilisterial S. lutetiensis strains should be validated further as potential costarter or adjunct cultures in Kefalotyri cheese. The prevalence of α-hemolytic pyogenic streptococci in raw milk, mainly S. parauberis in RM2, requires consideration in respect to subclinical mastitis in sheep and the farm hygiene overall.
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Affiliation(s)
- Eleni Sioziou
- Department of Dairy Research, Institute of Technology of Agricultural Products, Hellenic Agricultural Organization – DIMITRA, Ethnikis Antistaseos 3, Katsikas, Ioannina 45221, Greece
| | - Athanasia Kakouri
- Department of Dairy Research, Institute of Technology of Agricultural Products, Hellenic Agricultural Organization – DIMITRA, Ethnikis Antistaseos 3, Katsikas, Ioannina 45221, Greece
| | - Loulouda Bosnea
- Department of Dairy Research, Institute of Technology of Agricultural Products, Hellenic Agricultural Organization – DIMITRA, Ethnikis Antistaseos 3, Katsikas, Ioannina 45221, Greece
| | - John Samelis
- Department of Dairy Research, Institute of Technology of Agricultural Products, Hellenic Agricultural Organization – DIMITRA, Ethnikis Antistaseos 3, Katsikas, Ioannina 45221, Greece
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Filatava EJ, Liu Z, Xie J, Tran DB, Chen K, El Habbal N, Weinstock G, Zhou Y, Gregory KE. The preterm human milk microbiota fluctuates by postpartum week and is characterized by gestational age and maternal BMI. mBio 2023; 14:e0210623. [PMID: 37975676 PMCID: PMC10746270 DOI: 10.1128/mbio.02106-23] [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: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Despite a growing recognition that the type of nutrition received by preterm infants influences their intestinal microbiome and health outcomes, the microbiota of mother's own milk (MOM), pasteurized donor human milk (PDHM), and infant formula remain poorly characterized. In our study, we found that the structure of microbial communities, bacterial diversity, and relative abundances of specific genera were significantly different between MOM, PDHM, and formula. Additionally, our results suggest that the microbiota of MOM changes as a function of time and maternal factors. Lastly, we identified three lactotypes within MOM that have distinct microbial compositions and described the maternal factors associated with them. These findings set the stage for future research aimed at advancing our knowledge of the microbiota of preterm infant nutrition and the specific influence it may have on health outcomes.
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Affiliation(s)
| | - Zhongmao Liu
- University of Connecticut, Storrs, Connecticut, USA
| | - Jiaojiao Xie
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | | | - Kun Chen
- University of Connecticut, Storrs, Connecticut, USA
| | | | | | - Yanjiao Zhou
- University of Connecticut, Storrs, Connecticut, USA
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Ouamba AJK, Gagnon M, Varin T, Chouinard PY, LaPointe G, Roy D. Phylogenetic variation in raw cow milk microbiota and the impact of forage combinations and use of silage inoculants. Front Microbiol 2023; 14:1175663. [PMID: 38029116 PMCID: PMC10661925 DOI: 10.3389/fmicb.2023.1175663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction The microbiota of bulk tank raw milk is known to be closely related to that of microbial niches of the on-farm environment. Preserved forage types are partof this ecosystem and previous studies have shown variations in their microbial ecology. However, little is known of the microbiota of forage ration combinations and the transfer rates of associated species to milk. Methods We identified raw milk bacteria that may originate from forage rations encompassing either hay (H) or grass/legume silage uninoculated (GL) as the only forage type, or a combination of GL and corn silage uninoculated (GLC), or grass/legume and corn silage both inoculated (GLICI). Forage and milk samples collected in the fall and spring from 24 dairy farms were analyzed using 16S rRNA gene high-throughput sequencing following a treatment with propidium monoazide to account for viable cells. Results and discussion Three community types separating H, GL, and GLICI forage were identified. While the H community was co-dominated by Enterobacteriaceae, Microbacteriaceae, Beijerinckiaceae, and Sphingomonadaceae, the GL and GLICI communities showed high proportions of Leuconostocaceae and Acetobacteraceae, respectively. Most of the GLC and GLICI rations were similar, suggesting that in the mixed forage rations involving grass/legume and corn silage, the addition of inoculant in one or both types of feed does not considerably change the microbiota. Raw milk samples were not grouped in the same way, as the GLC milk was phylogenetically different from that of GLICI across sampling periods. Raw milk communities, including the GLICI group for which cows were fed inoculated forage, were differentiated by Enterobacteriaceae and other Proteobacteria, instead of by lactic acid bacteria. Of the 113 amplicon sequence variants (ASVs) shared between forage rations and corresponding raw milk, bacterial transfer rates were estimated at 18 to 31%. Silage-based forage rations, particularly those including corn, share more ASVs with raw milk produced on corresponding farms compared to that observed in the milk from cows fed hay. These results show the relevance of cow forage rations as sources of bacteria that contaminate milk and serve to advance our knowledge of on-farm raw milk contamination.
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Affiliation(s)
- Alexandre J. K. Ouamba
- Département des Sciences des Aliments, Laboratoire de Génomique Microbienne, Université Laval, Québec, QC, Canada
- Regroupement de Recherche pour Un Lait de Qualité Optimale (OpLait), Saint-Hyacinthe, QC, Canada
| | - Mérilie Gagnon
- Département des Sciences des Aliments, Laboratoire de Génomique Microbienne, Université Laval, Québec, QC, Canada
- Regroupement de Recherche pour Un Lait de Qualité Optimale (OpLait), Saint-Hyacinthe, QC, Canada
| | - Thibault Varin
- Département des Sciences des Aliments, Laboratoire de Génomique Microbienne, Université Laval, Québec, QC, Canada
| | - P. Yvan Chouinard
- Regroupement de Recherche pour Un Lait de Qualité Optimale (OpLait), Saint-Hyacinthe, QC, Canada
- Département des Sciences Animales, Université Laval, Québec, QC, Canada
| | - Gisèle LaPointe
- Regroupement de Recherche pour Un Lait de Qualité Optimale (OpLait), Saint-Hyacinthe, QC, Canada
- Department of Food Science, University of Guelph, Guelph, ON, Canada
| | - Denis Roy
- Département des Sciences des Aliments, Laboratoire de Génomique Microbienne, Université Laval, Québec, QC, Canada
- Regroupement de Recherche pour Un Lait de Qualité Optimale (OpLait), Saint-Hyacinthe, QC, Canada
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Delannoy S, Hoffer C, Tran ML, Madec JY, Brisabois A, Fach P, Haenni M. High throughput qPCR analyses suggest that Enterobacterales of French sheep and cow cheese rarely carry genes conferring resistances to critically important antibiotics for human medicine. Int J Food Microbiol 2023; 403:110303. [PMID: 37384974 DOI: 10.1016/j.ijfoodmicro.2023.110303] [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: 04/27/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 07/01/2023]
Abstract
Bacteria present in raw milk can carry acquired or intrinsic antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). However, only a few studies have evaluated raw milk cheese as a potential reservoir of ARGs. This study thus aimed at providing new data regarding resistance markers present in raw milk cheese. Sheep (n = 360) and cow (n = 360) cheese samples produced in France were incubated in buffered peptone water supplemented with acriflavin or novobiocin; as corroborated by 16S metabarcoding, samples were enriched in Gram-negative bacteria since Escherichia coli and Hafnia alvei respectively accounted for 40 % and 20 % of the samples' microbiota. Screening of the samples for the presence of 30 ARGs and 16 MGEs by high throughput qPCR array showed that nine ARGs conferring resistances to 1st-generation beta-lactams, aminoglycosides, trimethoprim/sulfonamides and tetracyclines occurred in >75 % of both sheep and cow samples. This is neither surprising nor alarming since these resistance genes are widely spread across the One Health human, animal and environmental sectors. Conversely, genes conferring resistances to last-generations cephalosporins were rarely identified, while those conferring resistances to carbapenems or amikacin, which are restricted to human use, were never detected. Multiple MGEs were detected, the most frequent ones being IncF plasmids, confirming the potential transmission of ARGs. Our results are in line with the few studies of the resistome of milk or milk cheese showing that genes conferring resistances to 1st-generation beta-lactams, aminoglycosides and tetracyclines families are widespread, while those conferring resistances to critically important antibiotics are rare or absent.
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Affiliation(s)
- Sabine Delannoy
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France.
| | - Corine Hoffer
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France
| | - Maï-Lan Tran
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France
| | - Jean-Yves Madec
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, 69007 Lyon, France
| | - Anne Brisabois
- Strategy and Programs Department, ANSES, 94700 Maisons-Alfort, France
| | - Patrick Fach
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France
| | - Marisa Haenni
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, 69007 Lyon, France
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Khasapane NG, Khumalo ZTH, Kwenda S, Nkhebenyane SJ, Thekisoe O. Characterisation of Milk Microbiota from Subclinical Mastitis and Apparently Healthy Dairy Cattle in Free State Province, South Africa. Vet Sci 2023; 10:616. [PMID: 37888568 PMCID: PMC10610705 DOI: 10.3390/vetsci10100616] [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: 08/13/2023] [Revised: 10/04/2023] [Accepted: 10/08/2023] [Indexed: 10/28/2023] Open
Abstract
Bovine mastitis is an inflammation of the udder tissue of the mammary gland brought on by microbial infections or physical damage. It is characterised by physical, chemical, and biological changes in the udder and milk. While several different bacterial species have been identified as causative agents of mastitis, many subclinical mastitis (SCM) cases remain culture-negative. The aim of this study was to characterise milk microbiota from SCM and apparently healthy dairy cows (non-SCM) by 16S rRNA sequencing. Alpha-diversity metrics showed significant differences between SCM cows and non-SCM counterparts. The beta-diversity metrics in the principal coordinate analysis significantly clustered samples by type (PERMANOVA test, p < 0.05), while non-metric dimensional scaling did not (PERMANOVA test, p = 0.07). The overall analysis indicated a total of 95 phyla, 33 classes, 82 orders, 124 families, 202 genera, and 119 bacterial species. Four phyla, namely Actinobacteriota, Bacteroidota, Firmicutes, and Proteobacteria collectively accounted for more than 97% of all sequencing reads from SCM and non-SCM cow samples. The most abundant bacterial classes were Actinobacteria, Bacilli, Bacteroidia, Clostridia, and Gammaproteobacteria in non-SCM cow samples, whilst SCM cow samples were mainly composed of Actinobacteria, Alphaproteobacteria, Bacilli, Clostridia, and Gammaproteobacteria. Dominant bacterial species in non-SCM cow samples were Anthropi spp., Pseudomonas azotoformans, P. fragi, Acinetobacter guillouiae, Enterococcus italicus, Lactococcus lactis, whilst P. azotoformans, Mycobacterium bovis, P. fragi, Acinetobacter guillouiae, and P. koreensis were dominant in the SCM cow samples. The current study found differences in bacterial species between SCM and non-SCM cow milk; hence, the need for detailed epidemiological studies.
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Affiliation(s)
- N. G. Khasapane
- Centre for Applied Food Safety and Biotechnology, Department of Life Sciences, Central University of Technology, 1 Park Road, Bloemfontein 9300, South Africa;
| | - Z. T. H. Khumalo
- ClinVet International, Study Management, Bainsvlei, Bloemfontein 9300, South Africa;
- Vectors and Vector-Borne Diseases Research Programme, Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, Pretoria 0110, South Africa
| | - S. Kwenda
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2192, South Africa;
| | - S. J. Nkhebenyane
- Centre for Applied Food Safety and Biotechnology, Department of Life Sciences, Central University of Technology, 1 Park Road, Bloemfontein 9300, South Africa;
| | - O. Thekisoe
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2531, South Africa;
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Hoving-Bolink RAH, Antonis AFG, te Pas MFW, Schokker D. An observational study of the presence and variability of the microbiota composition of goat herd milk related to mainstream and artisanal farm management. PLoS One 2023; 18:e0292650. [PMID: 37797079 PMCID: PMC10553829 DOI: 10.1371/journal.pone.0292650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 09/25/2023] [Indexed: 10/07/2023] Open
Abstract
Goat milk is produced on mainstream and artisanal farms. It was expected that the farm management may influence the microbial population of the milk. Therefore, we investigated the bacterial content and microbiota composition of raw milk in relation to Dutch goat farm management. After amplicon sequencing we analyzed the taxa at phylum and genus levels, and used the relative values enabling to provide information about the variation among the different samples. On ten farms our results indicated that the number of bacterial colony forming units and microbiota composition of the milk, directly after milking was variable among farms and not related to the farm management system. At the phylum level the phyla Firmicutes, Actinobacteria, Proteobacteria, and to a minor extend Bacteriodota were the dominant phyla in the raw goat milk, together usually comprising 90% of the total bacterial phyla. The most dominant genera were Staphylococcus, Pseudomonas, Lactococcus, Microbacteria, Acinetobacteria, and Corinebacteria. The number of bacterial phyla and genera does not differ between the mainstream and artisanal farms, although the Shannon index may be numerically higher in the mainstream farms as compared to artisanal farms. In addition, the variability is higher among artisanal farms, which may be due to less standardization of the management. The milk microbiota composition differed among farms. Repeated sampling of a farm showed that this changed over time. The lactic acid producing bacteria showed a similar pattern. Variable microbiota richness amount and diversity of microorganisms were present in different farming systems. We concluded that farm-specific management and sampling moment were the major determining factors for the milk microbiota composition.
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Caraba IV, Caraba MN. Effects of Feeding Management System on Milk Production and Milk Quality from Sheep of the Turcana Breed. Animals (Basel) 2023; 13:2977. [PMID: 37760377 PMCID: PMC10525387 DOI: 10.3390/ani13182977] [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: 08/21/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Milk and dairy products are among the foods preferred by consumers, as they are rich in nutrients, have high biological values, are easily accessible, and present a low risk to health. This study aimed to comparatively analyze the milk from sheep of the Turcana breed that were subjected to different feeding systems. The milk from the sheep was analyzed quantitatively and qualitatively; in this sense, the following were determined: daily milk production (DMY), physical parameters (pH, freezing point), chemical composition (lactose (L), fats (F), total proteins (TP), non-fat solids (Snf)), the content of heavy metals and trace elements (Zn, Cd, Cu, Fe, Mn, Pb), and microbiological parameters (the number of somatic cells (SCC), the total number of aerobic mesophilic germs that develop at 30 °C (NTG), the number of coliform bacteria (CT), the number of Staphylococcus aureus). Administration of the fodder complex produced, on the farm determined a slight quantitative increase in milk production, as well as in fat, protein and lactose content. The content of trace elements Zn, Fe, and Mn registered increases in milk samples from sheep that were administered the fodder complex. The content of heavy metals did not indicate any source of pollution in the grazing area. Furthermore, the microbiological parameters were within the allowed limits, indicating a good general state of health at the emergency level and the absence of microbiological contamination of the milk samples.
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Affiliation(s)
- Ion Valeriu Caraba
- Faculty of Bioengineering of Animal Resources, University of Life Sciences “King Mihai I” from Timisoara, Calea Aradului 119, RO 300645 Timisoara, Romania;
| | - Marioara Nicoleta Caraba
- Department Biology-Chemistry, Faculty of Chemistry-Biology-Geography, West University of Timisoara, Pestalozzi 16, RO 300315 Timisoara, Romania
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Ohno Y, Sekizuka T, Kuroda M, Ikeda T. Outbreaks of Campylobacteriosis Caused by Drinking Raw Milk in Japan: Evidence of Relationship Between Milk and Patients by Using Whole Genome Sequencing. Foodborne Pathog Dis 2023; 20:375-380. [PMID: 37471207 DOI: 10.1089/fpd.2023.0042] [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] [Indexed: 07/22/2023] Open
Abstract
Raw milk may contain some infectious bacteria and usually requires pasteurization before drinking. In this study, we report rare outbreaks of campylobacteriosis associated with raw milk in Japan, and the application of whole genome sequencing (WGS) to studies on foodborne diseases. In August 2018, there were three outbreaks of campylobacteriosis, presumably caused by the consumption of unpasteurized raw milk, derived from the same farm; thus, these three outbreaks seemed to be associated with a single contaminant at the farm. Therefore, we analyzed Campylobacter jejuni isolates obtained at the three locations using several genetic methods. The sequence type of each isolate, revealed by multilocus sequence typing, was ST-61, and the profile determined using pulsed-field gel electrophoresis was the same; however, neither method could distinguish these from previously obtained strains. Subsequently, we performed WGS and single nucleotide variant (SNV) analysis that provided evidence of clonality, indicating that C. jejuni contamination was attributed to the farm. As in this study, evidence suggests that SNV analysis provides molecular biological support in cases with sufficient epidemiological information. Hence, similar analytical methods may be used in other sporadic cases to elucidate the relevance of the cases.
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Affiliation(s)
- Yuta Ohno
- Department of Infectious Diseases, Hokkaido Institute of Public Health, Hokkaido, Japan
| | - Tsuyoshi Sekizuka
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Kuroda
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuya Ikeda
- Department of Infectious Diseases, Hokkaido Institute of Public Health, Hokkaido, Japan
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Long MM, Needs SH, Edwards AD. Dilution Reduces Sample Matrix Effects for Rapid, Direct, and Miniaturised Phenotypic Antibiotic Susceptibility Tests for Bovine Mastitis. Antibiotics (Basel) 2023; 12:1363. [PMID: 37760660 PMCID: PMC10525283 DOI: 10.3390/antibiotics12091363] [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: 07/20/2023] [Revised: 08/17/2023] [Accepted: 08/19/2023] [Indexed: 09/29/2023] Open
Abstract
The time-consuming nature of current methods for detecting antimicrobial resistance (AMR) to guide mastitis treatment and for surveillance, drives innovation towards faster, easier, and more portable technology. Rapid on-farm testing could guide antibiotic selection, reducing misuse that contributes to resistance. We identify challenges that arise when developing miniaturized antibiotic susceptibility tests (AST) for rapid on-farm use directly in milk. We experimentally studied three factors: sample matrix (specifically milk or spoiled milk); the commensal bacteria found in fresh bovine milk; and result time on the performance of miniaturised AST. Microfluidic "dip-and-test" devices made from microcapillary film (MCF) were able to monitor Gram-negative bacterial growth colourimetrically even in the presence of milk and yoghurt (used to simulate spoiled milk samples), as long as this sample matrix was diluted 1:5 or more in growth medium. Growth detection kinetics using resazurin was not changed by milk at final concentrations of 20% or lower, but a significant delay was seen with yoghurt above 10%. The minimum inhibitory concentration (MIC) for ciprofloxacin and gentamicin was increased in the presence of higher concentrations of milk and yoghurt. When diluted to 1% all observed MIC were within range, indicating dilution may be sufficient to avoid milk matrix interfering with microfluidic AST. We found a median commensal cell count of 6 × 105 CFU/mL across 40 healthy milk samples and tested if these bacteria could alter microfluidic AST. We found that false susceptibility may be observed at early endpoint times if testing some pathogen and commensal mixtures. However, such errors are only expected to occur when a susceptible commensal organism is present at higher cell density relative to the resistant pathogen, and this can be avoided by reading at later endpoints, leading to a trade-off between accuracy and time-to-result. We conclude that with further optimisation, and additional studies of Gram-positive organisms, it should be possible to obtain rapid results for microfluidic AST, but a trade-off is needed between time-to-result, sample dilution, and accuracy.
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Affiliation(s)
- Matthew Michael Long
- School of Pharmacy, University of Reading, Reading RG6 6DX, UK; (M.M.L.); (S.H.N.)
| | - Sarah Helen Needs
- School of Pharmacy, University of Reading, Reading RG6 6DX, UK; (M.M.L.); (S.H.N.)
| | - Alexander Daniel Edwards
- School of Pharmacy, University of Reading, Reading RG6 6DX, UK; (M.M.L.); (S.H.N.)
- Electronics and Computer Science, University of Southampton, Southampton SO17 1BJ, UK
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Abi Khalil R, Couderc C, Yvon S, Sicard D, Bigey F, Jard G, El Rammouz R, Abi Nakhoul P, Eutamène H, Ayoub MJ, Tormo H. Microbial Dynamics during labneh Ambaris Production in Earthenware Jars. Foods 2023; 12:3131. [PMID: 37628130 PMCID: PMC10453334 DOI: 10.3390/foods12163131] [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: 06/21/2023] [Revised: 08/04/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The responses of various microbial populations to modifications in the physicochemical properties of a food matrix, as well as interactions between these populations already present, are the main factors that shape microbial dynamics in that matrix. This work focused on the study of microbial dynamics during labneh Ambaris production, a traditional Lebanese concentrated fermented goat milk made in jars during 3 months. This was assessed in two earthenware jars at a production facility. DNA metabarcoding of the ITS2 region as well as the V3-V4 region of the 16S rRNA gene was used to characterize the fungal and bacterial communities, respectively. Viable bacterial isolates were also identified by Sanger sequencing of the V1-V4 region of the 16S rRNA gene. Our results showed that the dominant microorganisms identified within labneh Ambaris (Lactobacillus kefiranofaciens, Lentilactobacillus kefiri, Lactococcus lactis, Geotrichum candidum, Pichia kudriavzevii and Starmerella sp.) settle early in the product and remain until the end of maturation with varying abundances throughout fermentation. Microbial counts increased during early fermentation stage, and remained stable during mid-fermentation, then declined during maturation. While microbial compositions were globally comparable between the two jars during mid-fermentation and maturation stages, differences between the two jars were mainly detected during early fermentation stage (D0 until D10). No significant sensorial differences were observed between the final products made in the two jars. Neither coliforms nor Enterobacteriaceae were detected in their viable state, starting D7 in both jars, suggesting the antimicrobial properties of the product.
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Affiliation(s)
- Reine Abi Khalil
- Department of Food Sciences and Technologies, Faculty of Agricultural and Veterinary Sciences, Lebanese University, Beirut 14-6573, Lebanon; (R.A.K.); (P.A.N.)
- Département des Sciences de l’Agroalimentaire et de la Nutrition, INP EI-Purpan, Université de Toulouse, 75 voie du TOEIC, BP 57611, F-31076 Toulouse, CEDEX 3, France; (C.C.); (S.Y.); (G.J.); (H.E.)
| | - Christel Couderc
- Département des Sciences de l’Agroalimentaire et de la Nutrition, INP EI-Purpan, Université de Toulouse, 75 voie du TOEIC, BP 57611, F-31076 Toulouse, CEDEX 3, France; (C.C.); (S.Y.); (G.J.); (H.E.)
| | - Sophie Yvon
- Département des Sciences de l’Agroalimentaire et de la Nutrition, INP EI-Purpan, Université de Toulouse, 75 voie du TOEIC, BP 57611, F-31076 Toulouse, CEDEX 3, France; (C.C.); (S.Y.); (G.J.); (H.E.)
- Toxalim, UMR 1331, INRA, INP-ENVT, INP EI-Purpan, Université de Toulouse, F-31027 Toulouse, France
| | - Delphine Sicard
- SPO, INRAE, Institut Agro Montpellier, Université de Montpellier, F-34060 Montpellier, France; (D.S.); (F.B.)
| | - Frédéric Bigey
- SPO, INRAE, Institut Agro Montpellier, Université de Montpellier, F-34060 Montpellier, France; (D.S.); (F.B.)
| | - Gwenaelle Jard
- Département des Sciences de l’Agroalimentaire et de la Nutrition, INP EI-Purpan, Université de Toulouse, 75 voie du TOEIC, BP 57611, F-31076 Toulouse, CEDEX 3, France; (C.C.); (S.Y.); (G.J.); (H.E.)
| | - Rabih El Rammouz
- Department of Animal production, Faculty of Agricultural and Veterinary Sciences, Lebanese University, Beirut 14-6573, Lebanon;
| | - Pierre Abi Nakhoul
- Department of Food Sciences and Technologies, Faculty of Agricultural and Veterinary Sciences, Lebanese University, Beirut 14-6573, Lebanon; (R.A.K.); (P.A.N.)
| | - Hélène Eutamène
- Département des Sciences de l’Agroalimentaire et de la Nutrition, INP EI-Purpan, Université de Toulouse, 75 voie du TOEIC, BP 57611, F-31076 Toulouse, CEDEX 3, France; (C.C.); (S.Y.); (G.J.); (H.E.)
- Toxalim, UMR 1331, INRA, INP-ENVT, INP EI-Purpan, Université de Toulouse, F-31027 Toulouse, France
| | - Marie-José Ayoub
- Department of Food Sciences and Technologies, Faculty of Agricultural and Veterinary Sciences, Lebanese University, Beirut 14-6573, Lebanon; (R.A.K.); (P.A.N.)
| | - Hélène Tormo
- Département des Sciences de l’Agroalimentaire et de la Nutrition, INP EI-Purpan, Université de Toulouse, 75 voie du TOEIC, BP 57611, F-31076 Toulouse, CEDEX 3, France; (C.C.); (S.Y.); (G.J.); (H.E.)
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48
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Levante A, Bertani G, Marrella M, Mucchetti G, Bernini V, Lazzi C, Neviani E. The microbiota of Mozzarella di Bufala Campana PDO cheese: a study across the manufacturing process. Front Microbiol 2023; 14:1196879. [PMID: 37649628 PMCID: PMC10462780 DOI: 10.3389/fmicb.2023.1196879] [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: 03/30/2023] [Accepted: 06/30/2023] [Indexed: 09/01/2023] Open
Abstract
Introduction Mozzarella di Bufala Campana PDO cheese (MBC) is a globally esteemed Italian cheese. The traditional cheesemaking process of MBC relies on natural whey starter culture, water buffalo's milk, and the local agroecosystem. Methods In this study, the microbial ecology of intermediate samples of MBC production, coming from two dairies with slightly different cheesemaking technology (dairy M large producer, and dairy C medium-small), was investigated using 16S rRNA amplicon sequencing. This research aimed to provide insights into the dynamics of microbial consortia involved in various cheesemaking steps. Results and discussion All samples, except for raw buffalo milk, exhibited a core microbiome predominantly composed of Streptococcus spp. and Lactobacillus spp., albeit with different ratios between the two genera across the two MBC producers. Notably, the microbiota of the brine from both dairies, analyzed using 16S amplicon sequencing for the first time, was dominated by the Lactobacillus and Streptococcus genera, while only dairy C showed the presence of minor genera such as Pediococcus and Lentilactobacillus. Intriguingly, the final mozzarella samples from both producers displayed an inversion in the dominance of Lactobacillus spp. over Streptococcus spp. in the microbiota compared to curd samples, possibly attributable to the alleviation of thermal stress following the curd stretching step. In conclusion, the different samples from the two production facilities did not exhibit significant differences in terms of the species involved in MBC cheesemaking. This finding confirms that the key role in the MBC cheesemaking process lies with a small-sized microbiome primarily composed of Streptococcus and Lactobacillus spp.
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Affiliation(s)
- Alessia Levante
- Department of Food and Drug, University of Parma, Parma, Italy
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Romanò A, Ivanovic I, Segessemann T, Vazquez Rojo L, Widmer J, Egger L, Dreier M, Sesso L, Vaccani M, Schuler M, Frei D, Frey J, Ahrens CH, Steiner A, Graber HU. Elucidation of the Bovine Intramammary Bacteriome and Resistome from healthy cows of Swiss dairy farms in the Canton Tessin. Front Microbiol 2023; 14:1183018. [PMID: 37583512 PMCID: PMC10425240 DOI: 10.3389/fmicb.2023.1183018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/26/2023] [Indexed: 08/17/2023] Open
Abstract
Healthy, untreated cows of nine dairy herds from the Swiss Canton Tessin were analyzed three times within one year to identify the most abundant species of the intramammary bacteriome. Aseptically collected milk samples were cultured and bacteria identified using MALDI-TOF. Of 256 cows analyzed, 96% were bacteriologically positive and 80% of the 1,024 quarters were positive for at least one bacterial species. 84.5% of the quarters were healthy with somatic cell counts (SCC) < 200,000 cells/mL, whereas 15.5% of the quarters showed a subclinical mastitis (SCC ≥ 200,000 cells/mL). We could assign 1,288 isolates to 104 different bacterial species including 23 predominant species. Non-aureus staphylococci and mammaliicocci (NASM) were most prevalent (14 different species; 73.5% quarters). Staphylococcus xylosus and Mammaliicoccus sciuri accounted for 74.7% of all NASM isolates. To describe the intramammary resistome, 350 isolates of the predominant species were selected and subjected to short-read whole genome sequencing (WGS) and phenotypic antibiotic resistance profiling. While complete genomes of eight type strains were available, the remaining 15 were de novo assembled with long reads as a resource for the community. The 23 complete genomes served for reference-based assembly of the Illumina WGS data. Both chromosomes and mobile genetic elements were examined for antibiotic resistance genes (ARGs) using in-house and online software tools. ARGs were then correlated with phenotypic antibiotic resistance data from minimum inhibitory concentration (MIC). Phenotypic and genomic antimicrobial resistance was isolate-specific. Resistance to clindamycin and oxacillin was most frequently observed (65 and 30%) in Staphylococcus xylosus but could not be linked to chromosomal or plasmid-borne ARGs. However, in several cases, the observed antimicrobial resistance could be explained by the presence of mobile genetic elements like tetK carried on small plasmids. This represents a possible mechanism of transfer between non-pathogenic bacteria and pathogens of the mammary gland within and between herds. The-to our knowledge-most extensive bacteriome reported and the first attempt to link it with the resistome promise to profoundly affect veterinary bacteriology in the future and are highly relevant in a One Health context, in particular for mastitis, the treatment of which still heavily relies on antibiotics.
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Affiliation(s)
- Alicia Romanò
- Food Microbial Systems, Group Microbiological Safety of Foods of Animal Origin, Agroscope, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Ivana Ivanovic
- Food Microbial Systems, Group Microbiological Safety of Foods of Animal Origin, Agroscope, Bern, Switzerland
| | - Tina Segessemann
- SIB, Swiss Institute of Bioinformatics, Zürich, Switzerland
- Method Development and Analytics, Group Molecular Ecology, Agroscope, Zürich, Switzerland
| | - Laura Vazquez Rojo
- Food Microbial Systems, Group Microbiological Safety of Foods of Animal Origin, Agroscope, Bern, Switzerland
| | - Jérôme Widmer
- Method Development and Analytics, Group Biochemistry of Milk, Agroscope, Bern, Switzerland
| | - Lotti Egger
- Method Development and Analytics, Group Biochemistry of Milk, Agroscope, Bern, Switzerland
| | - Matthias Dreier
- Food Microbial Systems, Group Cultures, Biodiversity, and Terroir, Agroscope, Bern, Switzerland
| | - Lorenzo Sesso
- Clinic of Ruminants, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Michael Vaccani
- Clinic of Ruminants, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Martin Schuler
- SIB, Swiss Institute of Bioinformatics, Zürich, Switzerland
- Method Development and Analytics, Group Molecular Ecology, Agroscope, Zürich, Switzerland
| | - Daniel Frei
- Method Development and Analytics, Group Molecular Diagnostics, Genomics, and Bioinformatics, Agroscope, Wädenswil, Switzerland
| | - Juerg Frey
- Method Development and Analytics, Group Molecular Diagnostics, Genomics, and Bioinformatics, Agroscope, Wädenswil, Switzerland
| | - Christian H. Ahrens
- SIB, Swiss Institute of Bioinformatics, Zürich, Switzerland
- Method Development and Analytics, Group Molecular Ecology, Agroscope, Zürich, Switzerland
| | - Adrian Steiner
- Clinic of Ruminants, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Hans Ulrich Graber
- Food Microbial Systems, Group Microbiological Safety of Foods of Animal Origin, Agroscope, Bern, Switzerland
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50
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Keady MM, Jimenez RR, Bragg M, Wagner JCP, Bornbusch SL, Power ML, Muletz-Wolz CR. Ecoevolutionary processes structure milk microbiomes across the mammalian tree of life. Proc Natl Acad Sci U S A 2023; 120:e2218900120. [PMID: 37399384 PMCID: PMC10334807 DOI: 10.1073/pnas.2218900120] [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: 11/04/2022] [Accepted: 05/22/2023] [Indexed: 07/05/2023] Open
Abstract
Milk production is an ancient adaptation that unites all mammals. Milk contains a microbiome that can contribute to offspring health and microbial-immunological development. We generated a comprehensive milk microbiome dataset (16S rRNA gene) for the class Mammalia, representing 47 species from all placental superorders, to determine processes structuring milk microbiomes. We show that across Mammalia, milk exposes offspring to maternal bacterial and archaeal symbionts throughout lactation. Deterministic processes of environmental selection accounted for 20% of milk microbiome assembly processes; milk microbiomes were similar from mammals with the same host superorder (Afrotheria, Laurasiathera, Euarchontoglires, and Xenarthra: 6%), environment (marine captive, marine wild, terrestrial captive, and terrestrial wild: 6%), diet (carnivore, omnivore, herbivore, and insectivore: 5%), and milk nutrient content (sugar, fat, and protein: 3%). We found that diet directly and indirectly impacted milk microbiomes, with indirect effects being mediated by milk sugar content. Stochastic processes, such as ecological drift, accounted for 80% of milk microbiome assembly processes, which was high compared to mammalian gut and mammalian skin microbiomes (69% and 45%, respectively). Even amid high stochasticity and indirect effects, our results of direct dietary effects on milk microbiomes provide support for enteromammary trafficking, representing a mechanism by which bacteria are transferred from the mother's gut to mammary gland and then to offspring postnatally. The microbial species present in milk reflect both selective pressures and stochastic processes at the host level, exemplifying various ecological and evolutionary factors acting on milk microbiomes, which, in turn, set the stage for offspring health and development.
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Affiliation(s)
- Mia M. Keady
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC20008
- Nelson Institute for Environmental Studies, University of Wisconsin-Madison, Madison, WI53706
| | - Randall R. Jimenez
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC20008
- Science Team, International Union for Conservation of Nature, 11501San José, Costa Rica
| | - Morgan Bragg
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC20008
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA22030
| | - Jenna C. P. Wagner
- Nutrition Laboratory and Conservation Ecology Center, Smithsonian National Zoo and Conservation Biology Institute, National Zoological Park, Washington, DC20008
| | - Sally L. Bornbusch
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC20008
- Department of Nutrition Science, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC20008
| | - Michael L. Power
- Nutrition Laboratory and Conservation Ecology Center, Smithsonian National Zoo and Conservation Biology Institute, National Zoological Park, Washington, DC20008
| | - Carly R. Muletz-Wolz
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC20008
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