1
|
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of dPAB contamination of raw milk is important to understand cheese spoilage, long-term dPAB screening data are outdated, and studies taking into account different farm management parameters and their potential influence on dPAB levels are scarce.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.
Collapse
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.)
| |
Collapse
|
2
|
Güley Z, Fallico V, Cabrera-Rubio R, O’Sullivan D, Marotta M, Pennone V, Smith S, Beresford T. Diversity of the Microbiota of Traditional Izmir Tulum and Izmir Brined Tulum Cheeses and Selection of Potential Probiotics. Foods 2023; 12:3482. [PMID: 37761191 PMCID: PMC10528788 DOI: 10.3390/foods12183482] [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: 08/14/2023] [Revised: 09/09/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
High-throughput DNA sequencing (HTS) was used to study the microbial diversity of commercial traditional Izmir Tulum (IT) and Izmir Brined Tulum (IBT) cheeses from Izmir, Türkiye. Simultaneously, cultivation-dependent methods were used to isolate, identify and characterize bacterial strains displaying probiotic potential. At the phylum level, Firmicutes dominated the microbiota of both cheese types comprising >98% of the population. Thirty genera were observed, with Streptococcus being the most abundant genus and with Streptococcus thermophilus and S. infantarius subsp. infantarius being the most abundant species. Genera, including Bifidobacterium and Chryseobacterium, not previously associated with IT and IBT, were detected. IT cheeses displayed higher operational taxonomic units (OTUs; Richness) and diversity index (Simpson) than IBT cheeses; however, the difference between the diversity of the microbiota of IT and IBT cheese samples was not significant. Three Lacticaseibacillus paracasei strains isolated from IBT cheeses exhibited probiotic characteristics, which included capacity to survive under in vitro simulated gastrointestinal conditions, resistance to bile salts and potential to adhere to HT-29 human intestinal cells. These findings demonstrate that Tulum cheeses harbor bacterial genera not previously reported in this cheese and that some strains display probiotic characteristics.
Collapse
Affiliation(s)
- Ziba Güley
- Teagasc Food Research Centre, Moorepark, Fermoy, P61C996 Co. Cork, Ireland; (V.F.); (R.C.-R.); (D.O.); (M.M.); (V.P.); (S.S.); (T.B.)
- Department of Food Engineering, Alanya Alaaddin Keykubat University, 07425 Antalya, Türkiye
| | - Vincenzo Fallico
- Teagasc Food Research Centre, Moorepark, Fermoy, P61C996 Co. Cork, Ireland; (V.F.); (R.C.-R.); (D.O.); (M.M.); (V.P.); (S.S.); (T.B.)
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, P61C996 Co. Cork, Ireland; (V.F.); (R.C.-R.); (D.O.); (M.M.); (V.P.); (S.S.); (T.B.)
- APC Microbiome Ireland, University College Cork, T12Y120 Cork, Ireland
| | - Daniel O’Sullivan
- Teagasc Food Research Centre, Moorepark, Fermoy, P61C996 Co. Cork, Ireland; (V.F.); (R.C.-R.); (D.O.); (M.M.); (V.P.); (S.S.); (T.B.)
- School of Food and Nutritional Sciences, University College Cork, T12K8AF Cork, Ireland
| | - Mariarosaria Marotta
- Teagasc Food Research Centre, Moorepark, Fermoy, P61C996 Co. Cork, Ireland; (V.F.); (R.C.-R.); (D.O.); (M.M.); (V.P.); (S.S.); (T.B.)
| | - Vincenzo Pennone
- Teagasc Food Research Centre, Moorepark, Fermoy, P61C996 Co. Cork, Ireland; (V.F.); (R.C.-R.); (D.O.); (M.M.); (V.P.); (S.S.); (T.B.)
| | - Sandra Smith
- Teagasc Food Research Centre, Moorepark, Fermoy, P61C996 Co. Cork, Ireland; (V.F.); (R.C.-R.); (D.O.); (M.M.); (V.P.); (S.S.); (T.B.)
| | - Tom Beresford
- Teagasc Food Research Centre, Moorepark, Fermoy, P61C996 Co. Cork, Ireland; (V.F.); (R.C.-R.); (D.O.); (M.M.); (V.P.); (S.S.); (T.B.)
| |
Collapse
|
3
|
Dhital R, Mustapha A. DNA concentration by solid phase reversible immobilization improves its yield and purity, and detection time of E. coli O157:H7 in foods by high resolution melt curve qPCR. Food Control 2023. [DOI: 10.1016/j.foodcont.2022.109456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
4
|
Ahmadi A, Khezri A, Nørstebø H, Ahmad R. A culture-, amplification-independent, and rapid method for identification of pathogens and antibiotic resistance profile in bovine mastitis milk. Front Microbiol 2023; 13:1104701. [PMID: 36687564 PMCID: PMC9852903 DOI: 10.3389/fmicb.2022.1104701] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
Introduction Rapid and accurate diagnosis of causative pathogens in mastitis would minimize the imprudent use of antibiotics and, therefore, reduce the spread of antimicrobial resistance. Whole genome sequencing offers a unique opportunity to study the microbial community and antimicrobial resistance (AMR) in mastitis. However, the complexity of milk samples and the presence of a high amount of host DNA in milk from infected udders often make this very challenging. Methods Here, we tested 24 bovine milk samples (18 mastitis and six non-mastitis) using four different commercial kits (Qiagens' DNeasy® PowerFood® Microbial, Norgens' Milk Bacterial DNA Isolation, and Molzyms' MolYsis™ Plus and Complete5) in combination with filtration, low-speed centrifugation, nuclease, and 10% bile extract of male bovine (Ox bile). Isolated DNA was quantified, checked for the presence/absence of host and pathogen using PCR and sequenced using MinION nanopore sequencing. Bioinformatics analysis was performed for taxonomic classification and antimicrobial resistance gene detection. Results The results showed that kits designed explicitly for bacterial DNA isolation from food and dairy matrices could not deplete/minimize host DNA. Following using MolYsis™ Complete 5 + 10% Ox bile + micrococcal nuclease combination, on average, 17% and 66.5% of reads were classified as bovine and Staphylococcus aureus reads, respectively. This combination also effectively enriched other mastitis pathogens, including Escherichia coli and Streptococcus dysgalactiae. Furthermore, using this approach, we identified important AMR genes such as Tet (A), Tet (38), fosB-Saur, and blaZ. We showed that even 40 min of the MinION run was enough for bacterial identification and detecting the first AMR gene. Conclusion We implemented an effective method (sensitivity of 100% and specificity of 92.3%) for host DNA removal and bacterial DNA enrichment (both gram-negative and positive) directly from bovine mastitis milk. To the best of our knowledge, this is the first culture- and amplification-independent study using nanopore-based metagenomic sequencing for real-time detection of the pathogen (within 5 hours) and the AMR profile (within 5-9 hours), in mastitis milk samples. These results provide a promising and potential future on-farm adaptable approach for better clinical management of mastitis.
Collapse
Affiliation(s)
- Asal Ahmadi
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | | | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway,Institute of Clinical Medicine, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway,*Correspondence: Rafi Ahmad,
| |
Collapse
|
5
|
Tilocca B, Soggiu A, Iavarone F, Greco V, Putignani L, Ristori MV, Macari G, Spina AA, Morittu VM, Ceniti C, Piras C, Bonizzi L, Britti D, Urbani A, Figeys D, Roncada P. The Functional Characteristics of Goat Cheese Microbiota from a One-Health Perspective. Int J Mol Sci 2022; 23:ijms232214131. [PMID: 36430609 PMCID: PMC9698706 DOI: 10.3390/ijms232214131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
Abstract
Goat cheese is an important element of the Mediterranean diet, appreciated for its health-promoting features and unique taste. A pivotal role in the development of these characteristics is attributed to the microbiota and its continuous remodeling over space and time. Nevertheless, no thorough study of the cheese-associated microbiota using two metaomics approaches has previously been conducted. Here, we employed 16S rRNA gene sequencing and metaproteomics to explore the microbiota of a typical raw goat milk cheese at various ripening timepoints and depths of the cheese wheel. The 16S rRNA gene-sequencing and metaproteomics results described a stable microbiota ecology across the selected ripening timepoints, providing evidence for the microbiologically driven fermentation of goat milk products. The important features of the microbiota harbored on the surface and in the core of the cheese mass were highlighted in both compositional and functional terms. We observed the rind microbiota struggling to maintain the biosafety of the cheese through competition mechanisms and/or by preventing the colonization of the cheese by pathobionts of animal or environmental origin. The core microbiota was focused on other biochemical processes, supporting its role in the development of both the health benefits and the pleasant gustatory nuances of goat cheese.
Collapse
Affiliation(s)
- Bruno Tilocca
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Alessio Soggiu
- One Health Unit, Department of Biomedical, Surgical and Dental Sciences, University of Milano, Via della Commenda 10, 20133 Milano, Italy
| | - Federica Iavarone
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, Largo Vito, 00168 Rome, Italy
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Agostino Gemelli Foundation University Hospital IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Viviana Greco
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, Largo Vito, 00168 Rome, Italy
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Agostino Gemelli Foundation University Hospital IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Lorenza Putignani
- Unit of Parasitology, Unit of Human Microbiome, Bambino Gesù Children’s Hospital IRCCS, Piazza Sant’Onofrio, 4, 00165 Rome, Italy
| | - Maria Vittoria Ristori
- Unit of Parasitology, Unit of Human Microbiome, Bambino Gesù Children’s Hospital IRCCS, Piazza Sant’Onofrio, 4, 00165 Rome, Italy
| | | | - Anna Antonella Spina
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Valeria Maria Morittu
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Carlotta Ceniti
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Cristian Piras
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Luigi Bonizzi
- One Health Unit, Department of Biomedical, Surgical and Dental Sciences, University of Milano, Via della Commenda 10, 20133 Milano, Italy
| | - Domenico Britti
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Andrea Urbani
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, Largo Vito, 00168 Rome, Italy
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Agostino Gemelli Foundation University Hospital IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Paola Roncada
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
- Correspondence: ; Tel.: +39-096-1369-4284
| |
Collapse
|
6
|
Heo EJ, Kim HY, Suh SH, Moon JS. Comparison of DNA Extraction Methods for the Quantification of Listeria monocytogenes in Dairy Products by Real-Time Quantitative PCR>. J Food Prot 2022; 85:1531-1537. [PMID: 36084091 DOI: 10.4315/jfp-22-117] [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: 04/14/2022] [Accepted: 09/08/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT Listeria monocytogenes is a common foodborne pathogen affecting public health. Thus, detecting L. monocytogenes, even at low levels, in food matrices is essential. However, the current culture methods used for its detection and quantification are time consuming and difficult owing to background flora and interference by food matrices. DNA-based assays depend on DNA extraction and purification techniques. No optimal DNA extraction kit has been developed for analyzing L. monocytogenes in dairy products by real-time quantitative PCR (RT-qPCR). Therefore, in this study, we aimed to determine the efficiency of three DNA extraction kits for detecting L. monocytogenes in dairy products by RT-qPCR. We tested the efficiency of three commercial kits for DNA extraction from L. monocytogenes artificially inoculated in milk and dairy products. For the PrepSEQ rapid spin sample preparation kit and Exgene Cell SV mini, the limit of detection of was 100, 100, and 101 CFU/mL L. monocytogenes in milk, processed cheese, and infant formula, respectively, whereas that of the QIAamp DNA mini kit was 101, 103, and 102 CFU/mL, respectively. In addition, the Exgene Cell SV mini was better than the PrepSEQ rapid spin sample preparation kit for obtaining a standard curve for RT-qPCR of L. monocytogenes DNA in milk and dairy products, with a high correlation coefficient and amplification efficiency. The results of this study may be valuable for diagnostic laboratories and for developing an effective extraction method for processing food samples, such as dairy products, to subsequently detect and quantify L. monocytogenes by RT-qPCR. HIGHLIGHTS
Collapse
Affiliation(s)
- Eun Jeong Heo
- Ministry of Food and Drug Safety, 187, Osongsaengmyeong 2-ro, Cheongju, Chungbuk 28159, Republic of Korea
| | - Ha-Young Kim
- Animal and Plant Quarantine Agency, 177, Hyeoksin 8-ro, Gimcheon, Gyeongbuk 39660, Republic of Korea
| | - Soo Hwan Suh
- Ministry of Food and Drug Safety, 187, Osongsaengmyeong 2-ro, Cheongju, Chungbuk 28159, Republic of Korea
| | - Jin San Moon
- Animal and Plant Quarantine Agency, 177, Hyeoksin 8-ro, Gimcheon, Gyeongbuk 39660, Republic of Korea
| |
Collapse
|
7
|
Microbial Properties of Raw Milk throughout the Year and Their Relationships to Quality Parameters. Foods 2022; 11:foods11193077. [PMID: 36230153 PMCID: PMC9563975 DOI: 10.3390/foods11193077] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/26/2022] [Accepted: 10/01/2022] [Indexed: 01/16/2023] Open
Abstract
Raw milk microbiota is complex and influenced by many factors that facilitate the introduction of undesirable microorganisms. Milk microbiota is closely related to the safety and quality of dairy products, and it is therefore critical to characterize the variation in the microbial composition of raw milk. In this cross-sectional study, the variation in raw milk microbiota throughout the year (n = 142) from three farms in China was analyzed using 16S rRNA amplicon sequencing, including α and β diversity, microbial composition, and the relationship between microbiota and milk quality parameters. This aimed to characterize the contamination risk of raw milk throughout the year and the changes in quality parameters caused by contamination. Collection month had a significant effect on microbial composition; microbial diversity was higher in raw milk collected in May and June, while milk collected in October and December had the lowest microbial diversity. Microbiota composition differed significantly between milk collected in January−June, July−August, and September−December (p < 0.05). Bacterial communities represented in raw milk at the phylum level mainly included Proteobacteria, Firmicutes and Bacteroidota; Pseudomonas, Acinetobacter, Streptococcus and Lactobacillus were the most common genera. Redundancy analysis (RDA) found strong correlations between microbial distribution and titratable acidity (TA), fat, and protein. Many genera were significantly correlated with TA, for example Acinetobacter (R = 0.426), Enhydrobacter (R = 0.309), Chryseobacterium (R = 0.352), Lactobacillus (R = −0.326), norank_o__DTU014 (R = −0.697), norank_f__SC-I-84 (R = −0.678), and Subgroup_10 (R = −0.721). Additionally, norank_f__ Muribaculaceae was moderately negatively correlated with fat (R = −0.476) and protein (R = −0.513). These findings provide new information on the ecology of raw milk microbiota at the farm level and contribute to the understanding of the variation in raw milk microbiota in China.
Collapse
|
8
|
Ren Z, li N, Yu L, Zhao J, Zhang H, Chen W, Zhai Q. An Illumina MiSeq sequencing-based method using the mreB gene for high-throughput discrimination of Pseudomonas species in raw milk. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
9
|
Schwenker JA, Friedrichsen M, Waschina S, Bang C, Franke A, Mayer R, Hölzel CS. Bovine milk microbiota: Evaluation of different DNA extraction protocols for challenging samples. Microbiologyopen 2022; 11:e1275. [PMID: 35478279 PMCID: PMC9059235 DOI: 10.1002/mbo3.1275] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 03/09/2022] [Accepted: 03/09/2022] [Indexed: 01/04/2023] Open
Abstract
The use of an adequate protocol that accurately extracts microbial DNA from bovine milk samples is of importance for downstream analysis such as 16S ribosomal RNA gene sequencing. Although sequencing platforms such as Illumina are very common, there are reservations concerning reproducibility in challenging samples that combine low bacterial loads with high amounts of host DNA. The objective of this study was to evaluate six different DNA extraction protocols applied to four different prototype milk samples (low/high level of colony‐forming units [cfu] and somatic cells). DNA extracts were sequenced on Illumina MiSeq with primers for the hypervariable regions V1V2 and V3V4. Different protocols were evaluated by analyzing the yield and purity of DNA extracts and the number of clean reads after sequencing. Three protocols with the highest median number of clean reads were selected. To assess reproducibility, these extraction replicates were resequenced in triplicates (n = 120). The most reproducible results for α‐ and β‐diversity were obtained with the modified DNeasy Blood & Tissue kit after a chemical pretreatment plus resuspension of the cream fraction. The unmodified QIAamp DNA Mini kit performed particularly weak in the sample representing unspecific mastitis. These results suggest that pretreatment in combination with the modified DNeasy Blood & Tissue kit is useful in extracting microbial DNA from challenging milk samples. To increase reproducibility, we recommend that duplicates, if not triplicates, should be sequenced. We showed that high counts of somatic cells challenged DNA extraction, which shapes the need to apply modified extraction protocols.
Collapse
Affiliation(s)
- Julia A. Schwenker
- Department for Animal Hygiene and Health, Institute of Animal Breeding and Husbandry Christian‐Albrechts‐University Kiel Germany
| | - Meike Friedrichsen
- Department for Animal Hygiene and Health, Institute of Animal Breeding and Husbandry Christian‐Albrechts‐University Kiel Germany
| | - Silvio Waschina
- Institute of Human Nutrition and Food Science, Nutriinformatics Christian‐Albrechts‐University Kiel Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology Christian‐Albrechts‐University Kiel Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology Christian‐Albrechts‐University Kiel Germany
| | - Ricarda Mayer
- Department of Veterinary Sciences Ludwig‐Maximilians‐University Munich Oberschleißheim Germany
- GNA Biosolutions GmbH Martinsried Germany
| | - Christina S. Hölzel
- Department for Animal Hygiene and Health, Institute of Animal Breeding and Husbandry Christian‐Albrechts‐University Kiel Germany
| |
Collapse
|
10
|
Bagel A, Sergentet D. Shiga Toxin-Producing Escherichia coli and Milk Fat Globules. Microorganisms 2022; 10:microorganisms10030496. [PMID: 35336072 PMCID: PMC8953591 DOI: 10.3390/microorganisms10030496] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/09/2022] [Accepted: 02/17/2022] [Indexed: 02/04/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) are zoonotic Gram-negative bacteria. While raw milk cheese consumption is healthful, contamination with pathogens such as STEC can occur due to poor hygiene practices at the farm level. STEC infections cause mild to serious symptoms in humans. The raw milk cheese-making process concentrates certain milk macromolecules such as proteins and milk fat globules (MFGs), allowing the intrinsic beneficial and pathogenic microflora to continue to thrive. MFGs are surrounded by a biological membrane, the milk fat globule membrane (MFGM), which has a globally positive health effect, including inhibition of pathogen adhesion. In this review, we provide an update on the adhesion between STEC and raw MFGs and highlight the consequences of this interaction in terms of food safety, pathogen detection, and therapeutic development.
Collapse
Affiliation(s)
- Arthur Bagel
- ‘Bacterial Opportunistic Pathogens and Environment’ Research Team, Université de Lyon, UMR5557 Ecologie Microbienne Lyon, CNRS (National Center of Scientific Research), VetAgro Sup, Marcy-l’Etoile, 69280 Lyon, France;
| | - Delphine Sergentet
- ‘Bacterial Opportunistic Pathogens and Environment’ Research Team, Université de Lyon, UMR5557 Ecologie Microbienne Lyon, CNRS (National Center of Scientific Research), VetAgro Sup, Marcy-l’Etoile, 69280 Lyon, France;
- Laboratoire d’Etudes des Microorganismes Alimentaires Pathogènes-French National Reference Laboratory for Escherichia coli Including Shiga Toxin-Producing E. coli (NRL-STEC), VetAgro Sup—Campus Vétérinaire, Université de Lyon, Marcy-l’Etoile, 69280 Lyon, France
- Correspondence:
| |
Collapse
|
11
|
Pancza B, Szathmáry M, Gyurján I, Bánkuti B, Tudós Z, Szathmary S, Stipkovits L, Sipos-Kozma Z, Ásványi B, Varga L, Szenthe K, Bánáti F. A rapid and efficient DNA isolation method for qPCR-based detection of pathogenic and spoilage bacteria in milk. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
12
|
Bovine Milk Microbiota: Comparison among Three Different DNA Extraction Protocols To Identify a Better Approach for Bacterial Analysis. Microbiol Spectr 2021; 9:e0037421. [PMID: 34550002 PMCID: PMC8557886 DOI: 10.1128/spectrum.00374-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The bovine udder is colonized by a huge quantity of microorganisms that constitute the intramammary ecosystem, with a specific role in modulating not only udder homeostasis and mastitis susceptibility, but also the quality of the dairy products. However, generating high-quality bacterial DNA can be critical, especially starting from a complex biological matrix like milk, characterized by high fat, protein, and calcium contents. Here, bacterial DNA was recovered from a commercial ultra-high-temperature (UHT) milk sample artificially spiked with a predetermined mock community composition and from three bulk tank milk (raw milk) samples. The DNA was isolated using three different protocols to evaluate the effect of the extraction procedures on the milk microbiota composition. In the mock community experiment, the bacterial profiles generated by the three DNA extraction protocols were profoundly different, with the genera Staphylococcus, Lactobacillus, Listeria, and Salmonella underestimated by all the protocols. Only one protocol revealed values close to the expected abundances for Escherichia/Shigella spp., Bacillus spp., Enterococcus spp., and Pseudomonas spp. On the other hand, the nonspiked UHT milk sample exhibited a similar microbiota composition, revealing the prevalence of Acinetobacter spp., for all the DNA extraction protocols. For the raw milk samples, the three DNA extraction kits performed differently, revealing significant separations in both the microbial richness (alpha diversity) and composition (beta diversity). Our study highlights the presence of significant differences among these procedures, probably due to the different DNA extracting capacities and to the different properties of the milk samples, revealing that the selection of DNA extraction protocol is a critical point. IMPORTANCE The advance of high-throughput technologies has increased our knowledge of the world of microorganisms, especially of microbial populations inhabiting living animals. This study provides evidence that milk, as other complex sources, could be critical for generating high-quality DNA for microbiota analysis. In addition, it demonstrates that the microbial population highlighted by metagenomic studies changes in relation to different DNA extraction procedures, revealing that attention should be paid especially when comparing different studies.
Collapse
|
13
|
|
14
|
DNA Extraction and Host Depletion Methods Significantly Impact and Potentially Bias Bacterial Detection in a Biological Fluid. mSystems 2021; 6:e0061921. [PMID: 34128697 PMCID: PMC8574158 DOI: 10.1128/msystems.00619-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Untargeted sequencing of nucleic acids present in food can inform the detection of food safety and origin, as well as product tampering and mislabeling issues. The application of such technologies to food analysis may reveal valuable insights that are simply unobtainable by targeted testing, leading to the efforts of applying such technologies in the food industry. However, before these approaches can be applied, it is imperative to verify that the most appropriate methods are used at every step of the process: gathering of primary material, laboratory methods, data analysis, and interpretation. The focus of this study is on gathering the primary material, in this case, DNA. We used bovine milk as a model to (i) evaluate commercially available kits for their ability to extract nucleic acids from inoculated bovine milk, (ii) evaluate host DNA depletion methods for use with milk, and (iii) develop and evaluate a selective lysis-propidium monoazide (PMA)-based protocol for host DNA depletion in milk. Our results suggest that magnetically based nucleic acid extraction methods are best for nucleic acid isolation of bovine milk. Removal of host DNA remains a challenge for untargeted sequencing of milk, highlighting the finding that the individual matrix characteristics should always be considered in food testing. Some reported methods introduce bias against specific types of microbes, which may be particularly problematic in food safety, where the detection of Gram-negative pathogens and hygiene indicators is essential. Continuous efforts are needed to develop and validate new approaches for untargeted metagenomics in samples with large amounts of DNA from a single host. IMPORTANCE Tracking the bacterial communities present in our food has the potential to inform food safety and product origin. To do so, the entire genetic material present in a sample is extracted using chemical methods or commercially available kits and sequenced using next-generation platforms to provide a snapshot of the microbial composition. Because the genetic material of higher organisms present in food (e.g., cow in milk or beef, wheat in flour) is around 1,000 times larger than the bacterial content, challenges exist in gathering the information of interest. Additionally, specific bacterial characteristics can make them easier or harder to detect, adding another layer of complexity to this issue. In this study, we demonstrate the impact of using different methods for the ability to detect specific bacteria and highlight the need to ensure that the most appropriate methods are being used for each particular sample.
Collapse
|
15
|
Siebert A, Hofmann K, Staib L, Doll EV, Scherer S, Wenning M. Amplicon-sequencing of raw milk microbiota: impact of DNA extraction and library-PCR. Appl Microbiol Biotechnol 2021; 105:4761-4773. [PMID: 34059942 PMCID: PMC8195793 DOI: 10.1007/s00253-021-11353-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/29/2021] [Accepted: 05/16/2021] [Indexed: 01/12/2023]
Abstract
Abstract The highly complex raw milk matrix challenges the sample preparation for amplicon-sequencing due to low bacterial counts and high amounts of eukaryotic DNA originating from the cow. In this study, we optimized the extraction of bacterial DNA from raw milk for microbiome analysis and evaluated the impact of cycle numbers in the library-PCR. The selective lysis of eukaryotic cells by proteinase K and digestion of released DNA before bacterial lysis resulted in a high reduction of mostly eukaryotic DNA and increased the proportion of bacterial DNA. Comparative microbiome analysis showed that a combined enzymatic and mechanical lysis procedure using the DNeasy® PowerFood® Microbial Kit with a modified protocol was best suitable to achieve high DNA quantities after library-PCR and broad coverage of detected bacterial biodiversity. Increasing cycle numbers during library-PCR systematically altered results for species and beta-diversity with a tendency to overrepresentation or underrepresentation of particular taxa. To limit PCR bias, high cycle numbers should thus be avoided. An optimized DNA extraction yielding sufficient bacterial DNA and enabling higher PCR efficiency is fundamental for successful library preparation. We suggest that a protocol using ethylenediaminetetraacetic acid (EDTA) to resolve casein micelles, selective lysis of somatic cells, extraction of bacterial DNA with a combination of mechanical and enzymatic lysis, and restriction of PCR cycles for analysis of raw milk microbiomes is optimal even for samples with low bacterial numbers. Key points • Sample preparation for high-throughput 16S rRNA gene sequencing of raw milk microbiota. • Reduction of eukaryotic DNA by enzymatic digestion. • Shift of detected microbiome caused by high cycle numbers in library-PCR. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11353-4.
Collapse
Affiliation(s)
- Annemarie Siebert
- Chair of Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Katharina Hofmann
- Chair of Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Lena Staib
- Chair of Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Etienne V Doll
- Chair of Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Siegfried Scherer
- Chair of Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Mareike Wenning
- Chair of Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany. .,Bavarian Health and Food Safety Authority, Veterinärstraße 2, 85764, Oberschleissheim, Germany.
| |
Collapse
|
16
|
Castellanos-Rozo J, Pérez Pulido R, Grande MJ, Lucas R, Gálvez A. Potentially pathogenic bacteria isolated from Paipa cheese and its susceptibility profiles to antibiotics and biocides. Braz J Microbiol 2021; 52:1535-1543. [PMID: 34050446 DOI: 10.1007/s42770-021-00522-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 05/04/2021] [Indexed: 11/24/2022] Open
Abstract
The objective of this work was to evaluate the microbiological quality of cheese produced by formal and informal micro-enterprises in Paipa, Colombia, to isolate potentially pathogenic bacteria and to determine their prevalence and resistance to antimicrobials such as antibiotics and biocides. Sixteen micro-enterprises of the seventy existing in the region were sampled during 3 years. Viable concentrations of aerobic mesophiles, total and fecal coliforms, Salmonella sp., Listeria monocytogenes, Staphylococcus sp., yeasts, and molds were determined. Seventy-three bacterial isolates were identified by 16S rRNA gene sequencing. The susceptibility of the isolates to antibiotics and biocides was determined. The results indicated that between 98 and 100% of the cheese samples (n = 48 samples) of formal and informal micro-enterprises presented populations of total and fecal coliforms and Staphylococcus sp. above the limits established by Colombian regulations and varied according to the micro-enterprise. The results also indicated that 56% of Staphylococcus isolates were S. aureus. L. monocytogenes was positive in 38% of the samples. Salmonella sp. was not detected. The coliforms that prevailed were Escherichia coli (25%), Citrobacter freundii (14%), and Proteus mirabilis (8%). All L. monocytogenes were sensitive to ampicillin but resistant to erythromycin and trimethoprim-sulfamethoxazole. S. aureus isolates were susceptible to most antibiotics, except tetracycline and erythromycin (7% resistance). Likewise, 30% of coliforms (n = 36) were multidrug-resistant to antibiotics but susceptible to biocides.
Collapse
Affiliation(s)
- José Castellanos-Rozo
- Department of Biology and Microbiology, Faculty of Sciences and Engineering, Universidad de Boyacá, 150003, Tunja, Colombia
| | - Rubén Pérez Pulido
- Microbiology Division, Department of Health Sciences, Faculty of Experimental Sciences, University of Jaén, 23071, Jaén, Spain
| | - Mª José Grande
- Microbiology Division, Department of Health Sciences, Faculty of Experimental Sciences, University of Jaén, 23071, Jaén, Spain
| | - Rosario Lucas
- Microbiology Division, Department of Health Sciences, Faculty of Experimental Sciences, University of Jaén, 23071, Jaén, Spain
| | - Antonio Gálvez
- Microbiology Division, Department of Health Sciences, Faculty of Experimental Sciences, University of Jaén, 23071, Jaén, Spain.
| |
Collapse
|
17
|
Kamilari E, Efthymiou M, Anagnostopoulos DA, Tsaltas D. Cyprus Sausages' Bacterial Community Identification Through Metataxonomic Sequencing: Evaluation of the Impact of Different DNA Extraction Protocols on the Sausages' Microbial Diversity Representation. Front Microbiol 2021; 12:662957. [PMID: 34079530 PMCID: PMC8165277 DOI: 10.3389/fmicb.2021.662957] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/29/2021] [Indexed: 12/11/2022] Open
Abstract
Cyprus traditional sausages from the Troodos mountainous region of Pitsilia gained the protected geographical indication (PGI) designation from the European Committee (EU 2020/C 203/06). Still, we lack authentication protocols for the distinction of “Pitsilia” from industrially produced Cyprus sausages. Microbial activity is an essential contributor to traditional sausages’ sensorial characteristics, but whether the microbial patterns might be associated with the area of production is unclear. In the present research, we applied high-throughput sequencing (HTS) to provide a linkage between the area of production and Cyprus sausages’ bacterial diversity. To strengthen our findings, we used three different DNA extraction commercial kits: (i) the DNeasy PowerFood Microbial Kit (QIAGEN); (ii) the NucleoSpin Food Kit (MACHEREY-NAGEL); and (iii) the blackPREP Food DNA I Kit (Analytik Jena), in which we applied three different microbial cell wall lysis modifications. The modifications included heat treatment, bead beating, and enzymatic treatment. Results regarding metagenomic sequencing were evaluated in terms of number of reads, alpha diversity indexes, and taxonomic composition. The efficacy of each method of DNA isolation was assessed quantitatively based on the extracted DNA yield and the obtained copy number of (a) the 16S rRNA gene, (b) the internal transcribed spacer (ITS) region, and (c) three Gram-positive bacteria that belong to the genera Latilactobacillus (formerly Lactobacillus), Bacillus, and Enterococcus via absolute quantification using qPCR. Compared with some examined industrial sausages, Pitsilia sausages had significantly higher bacterial alpha diversity (Shannon and Simpson indexes). Principal coordinates analysis separated the total bacterial community composition (beta diversity) of the three Pitsilia sausages from the industrial sausages, with the exception of one industrial sausage produced in Pitsilia, according to the manufacturer. Although the eight sausages shared the abundant bacterial taxa based on 16S rDNA HTS, we observed differences associated with bacterial diversity representation and specific genera. The findings indicate that the microbial communities may be used as an additional tool for identifying of the authenticity of Cypriot sausages.
Collapse
Affiliation(s)
- Eleni Kamilari
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
| | - Marina Efthymiou
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
| | - Dimitrios A Anagnostopoulos
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
| | - Dimitrios Tsaltas
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
| |
Collapse
|
18
|
Microbiological and Metagenomic Characterization of a Retail Delicatessen Galotyri-Like Fresh Acid-Curd Cheese Product. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7020067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
This study evaluated the microbial quality, safety, and ecology of a retail delicatessen Galotyri-like fresh acid-curd cheese traditionally produced by mixing fresh natural Greek yogurt with ‘Myzithrenio’, a naturally fermented and ripened whey cheese variety. Five retail cheese batches (mean pH 4.1) were analyzed for total and selective microbial counts, and 150 presumptive isolates of lactic acid bacteria (LAB) were characterized biochemically. Additionally, the most and the least diversified batches were subjected to a culture-independent 16S rRNA gene sequencing analysis. LAB prevailed in all cheeses followed by yeasts. Enterobacteria, pseudomonads, and staphylococci were present as <100 viable cells/g of cheese. The yogurt starters Streptococcus thermophilus and Lactobacillus delbrueckii were the most abundant LAB isolates, followed by nonstarter strains of Lactiplantibacillus, Lacticaseibacillus, Enterococcus faecium, E. faecalis, and Leuconostoc mesenteroides, whose isolation frequency was batch-dependent. Lactococcus lactis isolates were sporadic, except for one cheese batch. However, Lactococcus lactis, Enterobacteriaceae, Vibrionaceae, Salinivibrio, and Shewanellaceae were detected at fairly high relative abundances culture-independently, despite the fact that their viable counts in the cheeses were low or undetectable. Metagenomics confirmed the prevalence of S. thermophilus and Lb. delbrueckii. Overall, this delicatessen Galotyri-like cheese product was shown to be a rich pool of indigenous nonstarter LAB strains, which deserve further biotechnological investigation.
Collapse
|
19
|
Torrez Lamberti MF, Harrison NA, Bendixen MM, DeBose-Scarlett EM, Thompson SC, Neu J, Parker LA, Lorca GL. Frozen Mother's Own Milk Can Be Used Effectively to Personalize Donor Human Milk. Front Microbiol 2021; 12:656889. [PMID: 33936012 PMCID: PMC8079756 DOI: 10.3389/fmicb.2021.656889] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/04/2021] [Indexed: 01/04/2023] Open
Abstract
Feeding preterm infants mother's own milk (MOM) lowers rates of sepsis, decreases necrotizing enterocolitis, and shortens hospital stay. In the absence of freshly expressed MOM, frozen MOM (FMOM) is provided. When MOM is unavailable, preterm infants are often fed pasteurized donor human milk (DHM), rendering it devoid of beneficial bacteria. We have previously reported that when MOM is inoculated into DHM to restore the live microbiota [restored milk (RM)], a similar microbial diversity to MOM can be achieved. Yet, it is unknown if a similar diversity to MOM can be obtained when FMOM is inoculated into DHM. The goal of this study was to determine whether a similar microbial composition to MOM could be obtained when FMOM is used to personalize DHM. To this end, a fresh sample of MOM was obtained and divided into fresh and frozen fractions. MOM and FMOM were inoculated into DHM at different dilutions: MOM/FMOM 10% (RM/FRM10) and MOM/FMOM 30% (RM/FRM30) and incubated at 37°C. At different timepoints, culture-dependent and culture-independent techniques were performed. Similar microbiota expansion and alpha diversity were observed in MOM, RM10, and RM30 whether fresh or frozen milk was used as the inoculum. To evaluate if microbial expansion would result in an abnormal activation on the innate immune system, Caco-2 epithelial cells were exposed to RM/FRM to compare interleukin 8 levels with Caco-2 cells exposed to MOM or DHM. It was found that RM samples did not elicit a significant increase in IL-8 levels when compared to MOM or FMOM. These results suggest that FMOM can be used to inoculate DHM if fresh MOM is unavailable or limited in supply, allowing both fresh MOM and FMOM to be viable options in a microbial restoration strategy.
Collapse
Affiliation(s)
- Monica F. Torrez Lamberti
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Natalie A. Harrison
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Marion M. Bendixen
- College of Nursing, University of Florida, Gainesville, FL, United States
| | - Evon M. DeBose-Scarlett
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Sharon C. Thompson
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Josef Neu
- Division of Neonatology, Department of Pediatrics, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Leslie Ann Parker
- College of Nursing, University of Florida, Gainesville, FL, United States
| | - Graciela L. Lorca
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| |
Collapse
|
20
|
Impact of DNA extraction methods on 16S rRNA-based profiling of bacterial communities in cheese. J Microbiol Methods 2021; 184:106210. [PMID: 33774112 DOI: 10.1016/j.mimet.2021.106210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 11/21/2022]
Abstract
Numerous factors associated with sample preparation, DNA extraction, primer choice, sequencing platform and data analysis can affect the accuracy of 16S rRNA sequencing results. The DNA extraction method is considered critical for the success of sequencing as it can be the source of considerable variations in the analysis of the microbiome. In this study, the impact of various DNA extraction methods on the results of analysis of bacterial communities in cheese was evaluated. DNA was isolated from Mozzarella as a model cheese using optimized bead-based homogenization followed by different extraction procedures. Five commercial kits and two open-formula DNA extraction protocols were evaluated for amplicon sequencing of a 16S rRNA fragment of ~1460 bp. In addition, model cheese samples artificially contaminated by defined concentrations of Listeria monocytogenes and Escherichia coli, as representatives of Gram positive and Gram negative bacteria, were analysed. Six out of seven DNA extraction procedures were found to be able to provide amplifiable bacterial DNA suitable for 16S rRNA sequence analysis, but individual extraction procedures led to variable results. In particular, lysis supported with bead-beating led to a higher proportion of G+ bacteria in relative abundance profiles, probably because of the more efficient cell wall disruption. Artificially added bacterial species were reliably detected with a quantitative response. The results demonstrated a risk in comparing the data on bacterial communities in cheese when different DNA extraction protocols are used and highlighted the need to choose a standardized approach when comparison across multiple sequencing runs is required.
Collapse
|
21
|
Dreier M, Berthoud H, Shani N, Wechsler D, Junier P. Development of a High-Throughput Microfluidic qPCR System for the Quantitative Determination of Quality-Relevant Bacteria in Cheese. Front Microbiol 2021; 11:619166. [PMID: 33488561 PMCID: PMC7817891 DOI: 10.3389/fmicb.2020.619166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/08/2020] [Indexed: 11/13/2022] Open
Abstract
The composition of the cheese microbiome has an important impact on the sensorial quality and safety of cheese. Therefore, much effort has been made to investigate the microbial community composition of cheese. Quantitative real-time polymerase chain reaction (qPCR) is a well-established method for detecting and quantifying bacteria. High-throughput qPCR (HT-qPCR) using microfluidics brings further advantages by providing fast results and by decreasing the cost per sample. We have developed a HT-qPCR approach for the rapid and cost-efficient quantification of microbial species in cheese by designing qPCR assays targeting 24 species/subspecies commonly found in cheese. Primer pairs were evaluated on the Biomark (Fluidigm) microfluidic HT-qPCR system using DNA from single strains and from artificial mock communities. The qPCR assays worked efficiently under identical PCR conditions, and the validation showed satisfying inclusivity, exclusivity, and amplification efficiencies. Preliminary results obtained from the HT-qPCR analysis of DNA samples of model cheeses made with the addition of adjunct cultures confirmed the potential of the microfluidic HT-qPCR system to screen for selected bacterial species in the cheese microbiome. HT-qPCR data of DNA samples of two downgraded commercial cheeses showed that this approach provides valuable information that can help to identify the microbial origin of quality defects. This newly developed HT-qPCR system is a promising approach that will allow simultaneous monitoring of quality-relevant species in fermented foods with high bacterial diversity, thereby opening up new perspectives for the control and assurance of high product quality.
Collapse
Affiliation(s)
- Matthias Dreier
- Agroscope, Bern, Switzerland.,Laboratory of Microbiology, University of Neuchâtel, Neuchâtel, Switzerland
| | | | | | | | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel, Neuchâtel, Switzerland
| |
Collapse
|
22
|
Lyons KE, Fouhy F, O’ Shea C, Ryan CA, Dempsey EM, Ross RP, Stanton C. Effect of storage, temperature, and extraction kit on the phylogenetic composition detected in the human milk microbiota. Microbiologyopen 2021; 10:e1127. [PMID: 33373099 PMCID: PMC7841076 DOI: 10.1002/mbo3.1127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 01/10/2023] Open
Abstract
Human milk is considered the optimum feeding regime for newborns and is a source of bacteria for the developing infant gastrointestinal tract. However, as with all low biomass samples, standardization across variabilities such as sample collection, storage, and extraction methods is needed to eliminate discrepancies in microbial composition across studies. The aim of this study was to investigate how different storage methods, temperatures, preservatives, and extraction kits influence the human milk microbiome, compared to fresh samples. Breast milk samples were processed via six different methods: fresh (Method 1), frozen at -80°C (Method 2), treated with RNAlater and stored at 4°C or -80°C (Methods 3 and 4), and treated with Milk Preservation Solution at room temperature (Methods 5 and 6). Methods 1-5 were extracted using PowerFoodTM Microbial DNA Isolation kit (Mobio), and Method 6 was extracted using Milk DNA Preservation and Isolation kit (Norgen BioTek). At genus level, the most abundant genera were shared across Methods 1-5. Samples frozen at -80°C had fewest significant changes while samples treated and extracted using Milk Preservation and Isolation kit had the most significant changes when compared to fresh samples. Diversity analysis indicated that variation in microbiota composition was related to the method and extraction kit used. This study highlighted that, when extraction from fresh milk samples is not an option, freezing at -80°C is the next best option to preserve the integrity of the milk microbiome. Furthermore, our results demonstrate that choice of extraction kit had a profound impact on the microbiota populations detected in milk.
Collapse
Affiliation(s)
- Katriona E. Lyons
- Teagasc Food Research CentreMoorepark, Fermoy, Co.CorkIreland
- School of MicrobiologyUniversity College CorkCorkIreland
| | - Fiona Fouhy
- Teagasc Food Research CentreMoorepark, Fermoy, Co.CorkIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
| | | | - C. Anthony Ryan
- APC Microbiome IrelandUniversity College CorkCorkIreland
- Department of NeonatologyCork University Maternity HospitalCorkIreland
| | - Eugene M. Dempsey
- APC Microbiome IrelandUniversity College CorkCorkIreland
- Department of NeonatologyCork University Maternity HospitalCorkIreland
| | - R. Paul Ross
- APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Catherine Stanton
- Teagasc Food Research CentreMoorepark, Fermoy, Co.CorkIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
| |
Collapse
|
23
|
Yap M, Feehily C, Walsh CJ, Fenelon M, Murphy EF, McAuliffe FM, van Sinderen D, O'Toole PW, O'Sullivan O, Cotter PD. Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome. Sci Rep 2020; 10:21665. [PMID: 33303873 PMCID: PMC7728742 DOI: 10.1038/s41598-020-78773-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/24/2020] [Indexed: 12/24/2022] Open
Abstract
Shotgun metagenomic sequencing is a valuable tool for the taxonomic and functional profiling of microbial communities. However, this approach is challenging in samples, such as milk, where a low microbial abundance, combined with high levels of host DNA, result in inefficient and uneconomical sequencing. Here we evaluate approaches to deplete host DNA or enrich microbial DNA prior to sequencing using three commercially available kits. We compared the percentage of microbial reads obtained from each kit after shotgun metagenomic sequencing. Using bovine and human milk samples, we determined that host depletion with the MolYsis complete5 kit significantly improved microbial sequencing depth compared to other approaches tested. Importantly, no biases were introduced. Additionally, the increased microbial sequencing depth allowed for further characterization of the microbiome through the generation of metagenome-assembled genomes (MAGs). Furthermore, with the use of a mock community, we compared three common classifiers and determined that Kraken2 was the optimal classifier for these samples. This evaluation shows that microbiome analysis can be performed on both bovine and human milk samples at a much greater resolution without the need for more expensive deep-sequencing approaches.
Collapse
Affiliation(s)
- Min Yap
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Conor Feehily
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Calum J Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Mark Fenelon
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | | | - Fionnuala M McAuliffe
- APC Microbiome Ireland, Cork, Ireland
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Paul W O'Toole
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Orla O'Sullivan
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.
- APC Microbiome Ireland, Cork, Ireland.
| |
Collapse
|
24
|
PCR-Based Direct Detection of Streptococcus uberis from Subclinical and Clinical Dairy Cattle Milk Samples. Vet Med Int 2020; 2020:8828624. [PMID: 33376590 PMCID: PMC7746883 DOI: 10.1155/2020/8828624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 11/20/2020] [Accepted: 11/25/2020] [Indexed: 11/30/2022] Open
Abstract
Streptococcus uberis is one of the leading causes worldwide of mastitis in the dairy industry, with the most likely sources of infection attributed to environmental reservoirs such as contaminated bedding materials. Early detection of those cases most likely to progress to clinical disease would lead to improved animal welfare, a critical component of overall health and productivity. A multiplex PCR-based diagnostic test was developed for detection of S. uberis directly from milk and targeting two genes previously identified as important for intramammary colonisation and persistence in dairy cattle. Results indicated the threshold for detection directly from milk was 20,000 CFU/ml and this was achieved without the need for preenrichment. In addition, S. uberis could be identified from milk samples collected during intramammary challenge studies, prior to clinical signs of infection and at much lower detection limits. The PCR test developed for confirmation of the presence of S. uberis directly from infected milk has potential value as a diagnostic test to identify early infection and/or to confirm that antibiotic therapy has been successful.
Collapse
|
25
|
de Melo Pereira GV, de Carvalho Neto DP, Maske BL, De Dea Lindner J, Vale AS, Favero GR, Viesser J, de Carvalho JC, Góes-Neto A, Soccol CR. An updated review on bacterial community composition of traditional fermented milk products: what next-generation sequencing has revealed so far? Crit Rev Food Sci Nutr 2020; 62:1870-1889. [PMID: 33207956 DOI: 10.1080/10408398.2020.1848787] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The emergence of next-generation sequencing (NGS) technologies has revolutionized the way to investigate the microbial diversity in traditional fermentations. In the field of food microbial ecology, different NGS platforms have been used for community analysis, including 454 pyrosequencing from Roche, Illumina's instruments and Thermo Fisher's SOLiD/Ion Torrent sequencers. These recent platforms generate information about millions of rDNA amplicons in a single running, enabling accurate phylogenetic resolution of microbial taxa. This review provides a comprehensive overview of the application of NGS for microbiome analysis of traditional fermented milk products worldwide. Fermented milk products covered in this review include kefir, buttermilk, koumiss, dahi, kurut, airag, tarag, khoormog, lait caillé, and suero costeño. Lactobacillus-mainly represented by Lb. helveticus, Lb. kefiranofaciens, and Lb. delbrueckii-is the most important and frequent genus with 51 reported species. In general, dominant species detected by culturing were also identified by NGS. However, NGS studies have revealed a more complex bacterial diversity, with estimated 400-600 operational taxonomic units, comprising uncultivable microorganisms, sub-dominant populations, and late-growing species. This review explores the importance of these discoveries and address related topics on workflow, NGS platforms, and knowledge bioinformatics devoted to fermented milk products. The knowledge that has been gained is vital in improving the monitoring, manipulation, and safety of these traditional fermented foods.
Collapse
Affiliation(s)
- Gilberto V de Melo Pereira
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Dão Pedro de Carvalho Neto
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Bruna L Maske
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Juliano De Dea Lindner
- Department of Food Science and Technology, Federal University of Santa Catarina (UFSC), Florianópolis, SC, Brazil
| | - Alexander S Vale
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Gabriel R Favero
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Jéssica Viesser
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Júlio C de Carvalho
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Aristóteles Góes-Neto
- Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Carlos R Soccol
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| |
Collapse
|
26
|
KOUR GURLEEN, CHANDRA MUDIT, KAUR GURPREET, NARANG DEEPTI, GUPTA DK. A simple modification in the DNA extraction process to extract good quality bacterial DNA from milk. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2020. [DOI: 10.56093/ijans.v90i4.104187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mastitis is the inflammation of the udder characterized by pathological changes in the mammary gland tissue. The most common treatment regimen involves administration of antibiotics depending upon culture and antibiotic sensitivity test. Culture and antibiotic sensitivity testing requires a minimum of 2-3 days, thus search for alternative tests to quicken identification of causative agent has gained lot of focus. In mastitis, milk is the ideal sample for the identification of causative agents as well as for performing DNA based tests such as PCR. Milk though easy to collect, harbour certain inhibitors affecting isolation of DNA. Also, the DNA extracted might contain certain associated ions which interfere in PCR. In the present study, DNA was extracted from milk by initially treating it with SDS and triton and later DNA was extracted using standard phenol chloroform method (M1). The efficiency of extraction by this method (M1) was compared with that of a kit (Power food microbial DNA isolation kit) based method (M2). The DNA extracted from both the methods was evaluated and compared among each other using genus specific PCR for E. coli, Klebsiella spp., Staphylococcus spp. and Streptococcus spp. along with various antibiotic resistance genes present in these bacteria. From the study, it could be concluded that DNA could be extracted successfully using SDS and triton method directly from the milk more efficiently and is cost effective when compared with kit-based method.
Collapse
|
27
|
Kingsbury JM, Soboleva TK. Evaluation of culture-based and molecular detection methods for Campylobacter in New Zealand raw cows' milk. J Appl Microbiol 2020; 130:478-492. [PMID: 32725959 DOI: 10.1111/jam.14798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 01/23/2023]
Abstract
AIMS This study evaluated the performance of a commercial molecular detection method (mericon Campylobacter triple kit real-time/quantitative (q)PCR) and a selective plating medium (R&F Campylobacter jejuni/Campylobacter coli Chromogenic Plating Medium (CCPM)) against a culture-based reference method (ISO 10272-1:2017 detection procedure B) for the detection of Campylobacter from raw milk enrichment broths. METHODS AND RESULTS New Zealand raw cows' milk and Ultra-High Temperature-processed milk samples were inoculated with 50, 125 and 500 colony forming units of C. jejuni and C. coli cocktail per analytical unit. Samples were tested for Campylobacter after 0, 24- and 48 h refrigeration. ISO 10272-1:2017 proved to be a sensitive detection method (77/80 positive samples); detection only failed for some milk samples tested 48 h postinoculation. CCPM was as effective as Cefoperazone Charcoal Deoxycholate Agar for selective plating of Campylobacter raw milk enrichments (78/80 positive samples). However, the qPCR detected Campylobacter in only 42/80 samples and qPCR reaction inhibition was observed. CONCLUSIONS The ISO 10272-1:2017 method was a more sensitive method for Campylobacter detection from raw milk than the mericon Campylobacter triple kit qPCR, and CCPM was a useful complementary medium to mCCDA where one of these media is required by the standard. SIGNIFICANCE AND IMPACT OF THE STUDY In regions where testing is required or recommended, optimized methods for Campylobacter detection from raw milk will reduce risk to the raw milk consumer. Although molecular methods are generally touted as a rapid alternative to culture, issues with inhibition due to matrix components mean that culture-based methods might provide the most sensitive option for Campylobacter detection in raw milk. Findings also emphasize the importance of minimizing the time between milk collection and testing for Campylobacter.
Collapse
Affiliation(s)
- J M Kingsbury
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - T K Soboleva
- New Zealand Food Safety, Ministry for Primary Industries, Wellington, New Zealand
| |
Collapse
|
28
|
Cheema AS, Stinson LF, Lai CT, Geddes DT, Payne MS. DNA extraction method influences human milk bacterial profiles. J Appl Microbiol 2020; 130:142-156. [PMID: 32654260 DOI: 10.1111/jam.14780] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/01/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022]
Abstract
AIMS To evaluate four DNA extraction methods to elucidate the most effective method for bacterial DNA recovery from human milk (HM). METHODS AND RESULTS Human milk DNA was extracted using the following methods: (i) Qiagen MagAttract Microbial DNA Isolation Kit (kit QM), (ii) Norgen Milk Bacterial DNA Isolation Kit (kit NM), (iii) Qiagen MagAttract Microbiome DNA/RNA Isolation Kit (kit MM) and (iv) TRIzol LS Reagent (method LS). The full-length 16S rRNA gene was sequenced. Kits MM and method LS were unable to extract detectable levels of DNA in 9/11 samples. Detectable levels of DNA were recovered from all samples using kits NM (mean = 0·68 ng μl-1 ) and QM (mean = 0·55 ng μl-1 ). For kits NM and QM, the greatest number of reads were associated with Staphylococcus epidermidis, Streptococcus vestibularis, Propionibacterium acnes, Veillonella dispar and Rothia mucilaginosa. Contamination profiles varied substantially between kits, with one bacterial species detected in negative extraction controls generated with kit QM and six with kit NM. CONCLUSIONS Kit QM is the most suitable of the kits tested for the extraction of bacterial DNA from human milk. SIGNIFICANCE AND IMPACT OF THE STUDY Choice of extraction method impacts the efficiency of bacterial DNA extraction from human milk and the resultant bacterial community profiles generated from these samples.
Collapse
Affiliation(s)
- A S Cheema
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - L F Stinson
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - C T Lai
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - D T Geddes
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - M S Payne
- Division of Obstetrics and Gynaecology, The University of Western Australia, Perth, WA, Australia
| |
Collapse
|
29
|
Preliminary Evidence of a Molecular Detection Method to Analyze Bacterial DNA as a Quality Indicator in Cosmetics. COSMETICS 2020. [DOI: 10.3390/cosmetics7030054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cosmetics are a category of widely consumed and distributed products, and their manufacture is always subject to specific guidelines. Quality Control (QC) tests provide information supporting the absence of injurious organisms and regarding the microbiological stability of cosmetics. The microbiological risk analysis is typically performed using the plate count method, which is a time-consuming and operator-dependent approach. Molecular technologies allow a deeper and more sensitive testing than traditional cultures. The demand for rapid and sensitive methods is recently increasing. The aim of our study was to compare different DNA extraction methods in order to detect and quantify bacterial load in cosmetics using a qPCR system. Known numbers of microorganisms were spiked into six different cosmetics to simulate contaminated samples. DNA was extracted with seven extraction kits and then quantified by real-time qPCR. Results revealed differences in terms of cell recovery, DNA yield, and quality. The bead-beating approaches were the most suitable in our molecular workflow and lead to good quality DNA for analysis by qPCR within four hours. Combined with mechanical extraction, qPCR may represent an efficient and easy method for microorganism identification in cosmetics, and can be automated. This approach also is also applicable for the detection of probiotics used as beneficial biological components in cosmetic products. The results of our molecular method provided preliminary evidences for the rapid identification of cells (10–100) and nucleic acids in complex preparations employed for human health, in compliance with regulatory limits. The suggested methodology is easy, fast, and sensitive. Its scalability allows serial microbiological evaluation at every manufacturing step.
Collapse
|
30
|
Grudlewska-Buda K, Skowron K, Gospodarek-Komkowska E. Comparison of the intensity of biofilm formation by Listeria monocytogenes using classical culture-based method and digital droplet PCR. AMB Express 2020; 10:75. [PMID: 32303851 PMCID: PMC7165217 DOI: 10.1186/s13568-020-01007-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 04/07/2020] [Indexed: 12/27/2022] Open
Abstract
Listeria monocytogenes is a Gram-positive bacterium, commonly found in food, water or sewage. This microorganism is capable of forming biofilm on different surfaces such as steel, glass, polypropylene etc. Recently an increase in cases of listeriosis has been noted, making L. monocytogenes the important health threat. Therefore, there is a need for rapid and sensitive detection of this pathogen. This study aimed to compare the number of L. monocytogenes cells recovered from the biofilm (prepared on steel and polypropylene) using the detection and amplification of the hlyA gene (droplet digital PCR, ddPCR) and the classical culture method. The research material consisted of 96 L. monocytogenes strains. A total of 58 isolates were obtained from clinical samples and 38 isolates derived from the municipal sewage treatment plant. Additionally, the reference strain ATCC®19111™ (WDCM00020) was used. The Pearson correlation coefficient for the results obtained by the classical culture-based method and ddPCR was 0.864 and 0.725, for biofilms produced on AISI 304 stainless steel surface and the polypropylene surface, respectively. Correlations were statistically significant (p ≤ 0.001), indicating that the ddPCR technique is an effective tool for the assessment of bacteria number in the biofilm.
Collapse
Affiliation(s)
- Katarzyna Grudlewska-Buda
- Department of Microbiology, Nicolaus Copernicus University in Toruń, Collegium Medicum of L. Rydygier in Bydgoszcz, Bydgoszcz, Poland
| | - Krzysztof Skowron
- Department of Microbiology, Nicolaus Copernicus University in Toruń, Collegium Medicum of L. Rydygier in Bydgoszcz, Bydgoszcz, Poland
| | - Eugenia Gospodarek-Komkowska
- Department of Microbiology, Nicolaus Copernicus University in Toruń, Collegium Medicum of L. Rydygier in Bydgoszcz, Bydgoszcz, Poland
| |
Collapse
|
31
|
Optimization of Preservation Methods Allows Deeper Insights into Changes of Raw Milk Microbiota. Microorganisms 2020; 8:microorganisms8030368. [PMID: 32151050 PMCID: PMC7142718 DOI: 10.3390/microorganisms8030368] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/29/2020] [Accepted: 03/03/2020] [Indexed: 12/17/2022] Open
Abstract
The temporal instability of raw milk microbiota drastically affects the reliability of microbiome studies. However, little is known about the microbial integrity in preserved samples. Raw cow milk samples were preserved with azidiol or bronopol and stored at 4 °C, or with dimethyl sulfoxide (DMSO) or a mixture of azidiol and DMSO and stored at −20 °C for up to 30 days. Aliquots of 5-, 10-, and 30-day post-storage were treated with propidium monoazide (PMA), then analyzed by sequencing the 16S rRNA gene V3-V4 and V6-V8 regions. The V6-V8 gave a higher richness and lower diversity than the V3-V4 region. After 5-day storage at 4 °C, the microbiota of unpreserved samples was characterized by a drastic decrease in diversity, and a significant shift in community structure. The treatment with azidiol and DMSO conferred the best community stabilization in preserved raw milk. Interestingly, the azidiol treatment performed as well for up to 10 days, thus appearing as a suitable alternative. However, neither azidiol nor bronopol could minimize fungal proliferation as revealed by PMA-qPCR assays. This study demonstrates the preservative ability of a mixture of azidiol and DMSO and provides deeper insights into the microbial changes occurring during the cold storage of preserved raw milk.
Collapse
|
32
|
Analysis of the Bacterial Diversity of Paipa Cheese (a Traditional Raw Cow's Milk Cheese from Colombia) by High-Throughput Sequencing. Microorganisms 2020; 8:microorganisms8020218. [PMID: 32041151 PMCID: PMC7074763 DOI: 10.3390/microorganisms8020218] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 12/18/2022] Open
Abstract
Background: Paipa cheese is a traditional, semi-ripened cheese made from raw cow’s milk in Colombia. The aim of this work was to gain insights on the microbiota of Paipa cheese by using a culture-independent approach. Method: two batches of Paipa cheese from three formal producers were sampled during ripening for 28 days. Total DNA from the cheese samples was used to obtain 16S rRNA gene sequences by using Illumina technology. Results: Firmicutes was the main phylum found in the cheeses (relative abundances: 59.2–82.0%), followed by Proteobacteria, Actinobacteria and Bacteroidetes. Lactococcus was the main genus, but other lactic acid bacteria (Enterococcus, Leuconostoc and Streptococcus) were also detected. Stapylococcus was also relevant in some cheese samples. The most important Proteobacteria were Enterobacteriaceae, Aeromonadaceae and Moraxellaceae. Enterobacter and Enterobacteriaceae (others) were detected in all cheese samples. Serratia and Citrobacter were detected in some samples. Aeromonas and Acinetobacter were also relevant. Other minor genera detected were Marinomonas, Corynebacterium 1 and Chryseobacterium. The principal coordinates analysis suggested that there were producer-dependent differences in the microbiota of Paipa cheeses. Conclusions: lactic acid bacteria are the main bacterial group in Paipa cheeses. However, other bacterial groups, including spoilage bacteria, potentially toxin producers, and bacteria potentially pathogenic to humans and/or prone to carry antimicrobial resistance genes are also relevant in the cheeses.
Collapse
|
33
|
Evaluation of DNA Extraction Methods for Culture-Independent Real-Time PCR-Based Detection of Listeria monocytogenes in Cheese. FOOD ANAL METHOD 2019. [DOI: 10.1007/s12161-019-01686-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
34
|
Gaur M, Vasudeva A, Singh A, Sharma V, Khurana H, Negi RK, Lee JK, Kalia VC, Misra R, Singh Y. Comparison of DNA Extraction Methods for Optimal Recovery of Metagenomic DNA from Human and Environmental Samples. Indian J Microbiol 2019; 59:482-489. [PMID: 31762512 DOI: 10.1007/s12088-019-00832-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 10/04/2019] [Indexed: 12/19/2022] Open
Abstract
Metagenomics is the study of gene pool of an entire community in a particular niche. This provides valuable information about the functionality of host-microbe interaction in a biological ecosystem. Efficient metagenomic DNA extraction is a critical pre-requisite for a successful sequencing run in a metagenomic study. Although isolation of human stool metagenomic DNA is fairly standardized, the same protocol does not work as efficiently in fecal DNA from other organisms. In this study, we report a comparison of manual and commercial DNA extraction methods for diverse samples such as human stool, fish gut and soil. Fishes are known to have variable microbial diversity based on their food habits, so the study included two different varieties of fishes. A modified protocol for effective isolation of metagenomic DNA from human milk samples is also reported, highlighting critical precautions. Recent studies have emphasized the importance of studying functionality of human milk metagenome to understand its influence on infants' health. While manual method works well with most samples and therefore can be a method of choice for testing new samples, broad-range commercial kit offers advantage of high purity and quality. DNA extraction of different samples would go a long way in unraveling the unexplored association between microbes and host in a biological system.
Collapse
Affiliation(s)
- Mohita Gaur
- 1Department of Zoology, University of Delhi, Delhi, India
| | | | - Anoop Singh
- 1Department of Zoology, University of Delhi, Delhi, India
| | - Vishal Sharma
- 1Department of Zoology, University of Delhi, Delhi, India
| | - Himani Khurana
- 1Department of Zoology, University of Delhi, Delhi, India
| | | | - Jung-Kul Lee
- 2Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Vipin Chandra Kalia
- 2Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Richa Misra
- 3Department of Zoology, Sri Venkateswara College, University of Delhi, Delhi, India
| | - Yogendra Singh
- 1Department of Zoology, University of Delhi, Delhi, India
| |
Collapse
|
35
|
Instrument-Free and Visual Detection of Salmonella Based on Magnetic Nanoparticles and an Antibody Probe Immunosensor. Int J Mol Sci 2019; 20:ijms20184645. [PMID: 31546808 PMCID: PMC6769488 DOI: 10.3390/ijms20184645] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 09/14/2019] [Accepted: 09/17/2019] [Indexed: 11/17/2022] Open
Abstract
Salmonella, a common foodborne pathogen, causes many cases of foodborne illness and poses a threat to public health worldwide. Immunological detection systems can be combined with nanoparticles to develop sensitive and portable detection technologies for timely screening of Salmonella infections. Here, we developed an antibody-probe-based immuno-N-hydroxysuccinimide (NHS) bead (AIB) system to detect Salmonella. After adding the antibody probe, Salmonella accumulated in the samples on the surfaces of the immuno-NHS beads (INBs), forming a sandwich structure (INB–Salmonella–probes). We demonstrated the utility of our AIB diagnostic system for detecting Salmonella in water, milk, and eggs, with a sensitivity of 9 CFU mL−1 in less than 50 min. The AIB diagnostic system exhibits highly specific detection and no cross-reaction with other similar microbial strains. With no specialized equipment or technical requirements, the AIB diagnostic method can be used for visual, rapid, and point-of-care detection of Salmonella.
Collapse
|
36
|
Sun L, Dicksved J, Priyashantha H, Lundh Å, Johansson M. Distribution of bacteria between different milk fractions, investigated using culture‐dependent methods and molecular‐based and fluorescent microscopy approaches. J Appl Microbiol 2019; 127:1028-1037. [DOI: 10.1111/jam.14377] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 06/25/2019] [Accepted: 07/01/2019] [Indexed: 12/22/2022]
Affiliation(s)
- L. Sun
- Department of Molecular Sciences Swedish University of Agricultural Sciences Uppsala Sweden
| | - J. Dicksved
- Department of Animal Nutrition and Management Swedish University of Agricultural Sciences Uppsala Sweden
| | - H. Priyashantha
- Department of Molecular Sciences Swedish University of Agricultural Sciences Uppsala Sweden
| | - Å. Lundh
- Department of Molecular Sciences Swedish University of Agricultural Sciences Uppsala Sweden
| | - M. Johansson
- Department of Molecular Sciences Swedish University of Agricultural Sciences Uppsala Sweden
| |
Collapse
|
37
|
Dahlberg J, Sun L, Persson Waller K, Östensson K, McGuire M, Agenäs S, Dicksved J. Microbiota data from low biomass milk samples is markedly affected by laboratory and reagent contamination. PLoS One 2019; 14:e0218257. [PMID: 31194836 PMCID: PMC6564671 DOI: 10.1371/journal.pone.0218257] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 05/29/2019] [Indexed: 12/15/2022] Open
Abstract
Discoveries of bacterial communities in environments that previously have been described as sterile have in recent years radically challenged the view of these environments. In this study we aimed to use 16S rRNA sequencing to describe the composition and temporal stability of the bacterial microbiota in bovine milk from healthy udder quarters, an environment previously believed to be sterile. Sequencing of the 16S rRNA gene is a technique commonly used to describe bacterial composition and diversity in various environments. With the increased use of 16S rRNA gene sequencing, awareness of methodological pitfalls such as biases and contamination has increased although not in equal amount. Evaluation of the composition and temporal stability of the microbiota in 288 milk samples was largely hampered by background contamination, despite careful and aseptic sample processing. Sequencing of no template control samples, positive control samples, with defined levels of bacteria, and 288 milk samples with various levels of bacterial growth, revealed that the data was influenced by contaminating taxa, primarily Methylobacterium. We observed an increasing impact of contamination with decreasing microbial biomass where the contaminating taxa became dominant in samples with less than 104 bacterial cells per mL. By applying a contamination filtration on the sequence data, the amount of sequences was substantially reduced but only a minor impact on number of identified taxa and by culture known endogenous taxa was observed. This suggests that data filtration can be useful for identifying biologically relevant associations in milk microbiota data.
Collapse
Affiliation(s)
- Josef Dahlberg
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
| | - Li Sun
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Karin Persson Waller
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute, Uppsala, Sweden
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Karin Östensson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mark McGuire
- Department of Animal and Veterinary Science, University of Idaho, Moscow, United States of America
| | - Sigrid Agenäs
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Johan Dicksved
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Uppsala, Sweden
| |
Collapse
|
38
|
Milk and Dairy Products. Food Microbiol 2019. [DOI: 10.1128/9781555819972.ch5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
39
|
Petrullo L, Jorgensen MJ, Snyder‐Mackler N, Lu A. Composition and stability of the vervet monkey milk microbiome. Am J Primatol 2019; 81:e22982. [DOI: 10.1002/ajp.22982] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 04/10/2019] [Accepted: 04/14/2019] [Indexed: 11/12/2022]
Affiliation(s)
- Lauren Petrullo
- Interdepartmental Doctoral Program in Anthropological SciencesStony Brook UniversityStony Brook NY
| | - Matthew J. Jorgensen
- Department of Pathology, Section on Comparative MedicineWake Forest School of MedicineWinston‐Salem NC
| | - Noah Snyder‐Mackler
- Department of PsychologyUniversity of WashingtonSeattle WA
- Center for Studies in Demography & EcologyUniversity of WashingtonSeattle WA
- Washington National Primate Research CenterUniversity of WashingtonSeattle WA
| | - Amy Lu
- Department of AnthropologyStony Brook UniversityStony Brook NY
| |
Collapse
|
40
|
Appelt S, Aly SS, Tonooka K, Glenn K, Xue Z, Lehenbauer TW, Marco ML. Development and comparison of loop-mediated isothermal amplification and quantitative polymerase chain reaction assays for the detection of Mycoplasma bovis in milk. J Dairy Sci 2019; 102:1985-1996. [DOI: 10.3168/jds.2018-15306] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/05/2018] [Indexed: 11/19/2022]
|
41
|
Peruzy M, Murru N, Yu Z, Cnockaert M, Joossens M, Proroga Y, Houf K. Determination of the microbiological contamination in minced pork by culture dependent and 16S amplicon sequencing analysis. Int J Food Microbiol 2019; 290:27-35. [DOI: 10.1016/j.ijfoodmicro.2018.09.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 09/14/2018] [Accepted: 09/28/2018] [Indexed: 12/22/2022]
|
42
|
Abstract
The milk microbiota is an intriguing area of research because milk with no bacterial growth in culture was long thought to be sterile. Recent DNA sequencing techniques have been developed that do not require bacteria to be culturable, and DNA from new bacteria have been reported in milk from dairy cow mammary glands with or without mastitis. Methodologies and results vary among research groups, and not enough is known about the milk microbiota for the results to be used for diagnosis or prognosis of mastitis.
Collapse
|
43
|
Xue Z, Kable ME, Marco ML. Impact of DNA Sequencing and Analysis Methods on 16S rRNA Gene Bacterial Community Analysis of Dairy Products. mSphere 2018; 3:e00410-18. [PMID: 30333179 PMCID: PMC6193606 DOI: 10.1128/msphere.00410-18] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 09/13/2018] [Indexed: 12/17/2022] Open
Abstract
DNA sequencing and analysis methods were compared for 16S rRNA V4 PCR amplicon and genomic DNA (gDNA) mock communities encompassing nine bacterial species commonly found in milk and dairy products. The two communities comprised strain-specific DNA that was pooled before (gDNA) or after (PCR amplicon) the PCR step. The communities were sequenced on the Illumina MiSeq and Ion Torrent PGM platforms and then analyzed using the QIIME 1 (UCLUST) and Divisive Amplicon Denoising Algorithm 2 (DADA2) analysis pipelines with taxonomic comparisons to the Greengenes and Ribosomal Database Project (RDP) databases. Examination of the PCR amplicon mock community with these methods resulted in operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) that ranged from 13 to 118 and were dependent on the DNA sequencing method and read assembly steps. The additional 4 to 109 OTUs/ASVs (from 9 OTUs/ASVs) included assignments to spurious taxa and sequence variants of the 9 species included in the mock community. Comparisons between the gDNA and PCR amplicon mock communities showed that combining gDNAs from the different strains prior to PCR resulted in up to 8.9-fold greater numbers of spurious OTUs/ASVs. However, the DNA sequencing method and paired-end read assembly steps conferred the largest effects on predictions of bacterial diversity, with effect sizes of 0.88 (Bray-Curtis) and 0.32 (weighted Unifrac), independent of the mock community type. Overall, DNA sequencing performed with the Ion Torrent PGM and analyzed with DADA2 and the Greengenes database resulted in the most accurate predictions of the mock community phylogeny, taxonomy, and diversity.IMPORTANCE Validated methods are urgently needed to improve DNA sequence-based assessments of complex bacterial communities. In this study, we used 16S rRNA PCR amplicon and gDNA mock community standards, consisting of nine, dairy-associated bacterial species, to evaluate the most commonly applied 16S rRNA marker gene DNA sequencing and analysis platforms used in evaluating dairy and other bacterial habitats. Our results show that bacterial metataxonomic assessments are largely dependent on the DNA sequencing platform and read curation method used. DADA2 improved sequence annotation compared with QIIME 1, and when combined with the Ion Torrent PGM DNA sequencing platform and the Greengenes database for taxonomic assignment, the most accurate representation of the dairy mock community standards was reached. This approach will be useful for validating sample collection and DNA extraction methods and ultimately investigating bacterial population dynamics in milk- and dairy-associated environments.
Collapse
Affiliation(s)
- Zhengyao Xue
- Department of Food Science & Technology, University of California, Davis, California, USA
| | - Mary E Kable
- Department of Food Science & Technology, University of California, Davis, California, USA
| | - Maria L Marco
- Department of Food Science & Technology, University of California, Davis, California, USA
| |
Collapse
|
44
|
THAKUR RASHMI, SINGH RANDHIR, KAUR SIMRANPREET, GILL JPS. Comparative evaluation of loop mediated isothermal amplification assay for rapid detection of Staphylococcus aureus. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2018. [DOI: 10.56093/ijans.v88i9.83542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A loop mediated isothermal amplification (LAMP) method for rapid detection of Staphylococcus aureus from milk using standard strain ATCC 33591 was optimized targeting thermonuclease (nuc) gene. LAMP protocol was optimized for detection of S. aureus at 62°C for 50 min in water bath. The analytical sensitivity of LAMP and qPCR was found to be equal, ca.102 CFU/ml, both in broth and spiked milk by commercial kit and phenol-chloroform-isoamyl method of DNA extraction, while the sensitivity of conventional PCR was low (ca. 103 and 104CFU/ml in broth and spiked milk samples, respectively), using kit method of DNA extraction. LAMP was 100% specific and in complete agreement with real time and conventional PCR. LAMP protocol optimized in the study was rapid and sensitive in detection of S. aureus in comparison to qPCR and PCR when kit method of DNA extraction was used. Application of LAMP for rapid detection of S. aureus on 126 field milk samples detected 93 milk samples positive out of 97 positive by culture without enrichment, hence giving sensitivity of 95.87%. Whereas, LAMP detected all 29 milk samples negative by culture as negative, thereby giving detection specificity of 100%. However, on enrichment of LAMP negative samples for four hours, LAMP could detect them positive for S. aureus. Enrichment of the milk sample for four hours enhanced the sensitivity of detection to 100% and detection limit to < 102 CFU/ml.
Collapse
|
45
|
Carafa I, Stocco G, Franceschi P, Summer A, Tuohy KM, Bittante G, Franciosi E. Evaluation of autochthonous lactic acid bacteria as starter and non-starter cultures for the production of Traditional Mountain cheese. Food Res Int 2018; 115:209-218. [PMID: 30599933 DOI: 10.1016/j.foodres.2018.08.069] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 08/10/2018] [Accepted: 08/20/2018] [Indexed: 11/25/2022]
Abstract
Lactococcus lactis subsp. lactis 68, Streptococcus thermophilus 93 and Lactobacillus rhamnosus BT68, previously isolated from Traditional Mountain (TM) cheese, were tested for the production of four experimental mountain cheeses, with the aim to assess their effectiveness in leading the TM-cheese-making process. Lactococcus lactis subsp. lactis 68 and Streptococcus thermophilus 93 were used as starter cultures, whereas Lactobacillus rhamnosus BT68 was used as non-starter culture. Three control (CTRL) cheeses were manufactured without adding any starter, according to the traditional cheese-making process; nine, cheeses were produced inoculating the vat milk with the starters (ST), starter and low concentration of non-starter culture (STLC), starter and high concentration of non-starter culture (STHC). Samples of vat milk, cheese after 24 h and 7 months ripening were processed for microbiological counts. Mesophilic cocci were dominant in all 24 h-cheese samples, while a dominance of both cocci and lactobacilli was observed after 7 months ripening. The total genomic DNA was extracted, and a fragment of V1-V3 region was amplified and pyrosequenced. Lactococci and streptococci were the most abundant species, and Lc. lactis ssp. lactis 68 affected the proliferation of milk-resident Lc. lactis ssp. cremoris, during the early fermentation. Lb. rhamnosus BT68 showed to be responsible in reducing the abundance of other Lactobacillus species. Moreover, it likely competed against Sc. thermophilus 93 for the same energetic sources, when added in concentration higher than 5 × 103 CFU/mL milk. The sensorial and fatty acid (FA) composition analysis were performed on cheese samples at the end of ripening, demonstrating that the inoculated cheeses had better sensorial characteristics (aspect, smell, taste, texture) than CTRL cheeses, and that Lb. rhamnosus BT68 at high concentration is related to the increase of short chain fatty acids and conjugated linoleic acid in cheese after 7 months ripening.
Collapse
Affiliation(s)
- Ilaria Carafa
- Research and Innovation Centre, AgriFood Quality and Nutrition Department, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010 San Michele all'Adige, Italy
| | - Giorgia Stocco
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - Piero Franceschi
- Department of Veterinary Science, University of Parma, Strada del Taglio, 10, 43126 Parma, Italy
| | - Andrea Summer
- Department of Veterinary Science, University of Parma, Strada del Taglio, 10, 43126 Parma, Italy
| | - Kieran Michael Tuohy
- Research and Innovation Centre, AgriFood Quality and Nutrition Department, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010 San Michele all'Adige, Italy
| | - Giovanni Bittante
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - Elena Franciosi
- Research and Innovation Centre, AgriFood Quality and Nutrition Department, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010 San Michele all'Adige, Italy.
| |
Collapse
|
46
|
Engel K, Sauer J, Jünemann S, Winkler A, Wibberg D, Kalinowski J, Tauch A, Caspers BA. Individual- and Species-Specific Skin Microbiomes in Three Different Estrildid Finch Species Revealed by 16S Amplicon Sequencing. MICROBIAL ECOLOGY 2018; 76:518-529. [PMID: 29282519 DOI: 10.1007/s00248-017-1130-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 12/12/2017] [Indexed: 05/16/2023]
Abstract
An animals' body is densely populated with bacteria. Although a large number of investigations on physiological microbial colonisation have emerged in recent years, our understanding of the composition, ecology and function of the microbiota remains incomplete. Here, we investigated whether songbirds have an individual-specific skin microbiome that is similar across different body regions. We collected skin microbe samples from three different bird species (Taeniopygia gutatta, Lonchura striata domestica and Stagonopleura gutatta) at two body locations (neck region, preen gland area). To characterise the skin microbes and compare the bacterial composition, we used high-throughput 16S rRNA amplicon sequencing. This method proved suitable for identifying the skin microbiome of birds, even though the bacterial load on the skin appeared to be relatively low. We found that across all species, the two evaluated skin areas of each individual harboured very similar microbial communities, indicative of an individual-specific skin microbiome. Despite experiencing the same environmental conditions and consuming the same diet, significant differences in the skin microbe composition were identified among the three species. The bird species differed both quantitatively and qualitatively regarding the observed bacterial taxa. Although each species harboured its own unique set of skin microbes, we identified a core skin microbiome among the studied species. As microbes are known to influence the host's body odour, our findings of an individual-specific skin microbiome might suggest that the skin microbiome in birds is involved in the odour production and could encode information on the host's genotype.
Collapse
Affiliation(s)
- Kathrin Engel
- Department of Animal Behaviour, Research Group Chemical Signalling, Bielefeld University, Konsequenz 45, 33615, Bielefeld, Germany.
| | - Jan Sauer
- Department of Animal Behaviour, Research Group Chemical Signalling, Bielefeld University, Konsequenz 45, 33615, Bielefeld, Germany.
| | - Sebastian Jünemann
- Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615, Bielefeld, Germany
- Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Anika Winkler
- Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615, Bielefeld, Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615, Bielefeld, Germany
| | - Andreas Tauch
- Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615, Bielefeld, Germany
| | - Barbara A Caspers
- Department of Animal Behaviour, Research Group Chemical Signalling, Bielefeld University, Konsequenz 45, 33615, Bielefeld, Germany
| |
Collapse
|
47
|
Vandera E, Tsirka G, Kakouri A, Koukkou AI, Samelis J. Approaches for enhancing in situ detection of enterocin genes in thermized milk, and selective isolation of enterocin-producing Enterococcus faecium from Baird-Parker agar. Int J Food Microbiol 2018; 281:23-31. [PMID: 29803907 DOI: 10.1016/j.ijfoodmicro.2018.05.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/21/2018] [Accepted: 05/20/2018] [Indexed: 11/24/2022]
Abstract
Enterococci are naturally selected for growth in thermized ewes'/goats' milk mixtures used for traditional cooked hard cheese processing in Greece. A culture-independent PCR-based approach was applied to detect the presence of enterocin-encoding genes in naturally culture-enriched thermized milk (TM). Portions of TM (63 °C, 30 s) collected from a commercial cheese plant before addition of starters were fermented at 37 °C for 48 h to facilitate growth of indigenous enterococci. The multiple enterocin-producing (m-Ent+) Enterococcus faecium KE82 and the nisin A-producing Lactococcus lactis subsp. cremoris M104 served as bacteriocin-positive inocula in separate TM treatments. The PCR results revealed a constant presence of the enterocin A, B and P genes in TM fermented naturally at 37 °C. Eleven out of 42 (26.2%) lactic isolates from the enriched TM cultures without inoculation were Ent+ E. faecium assigned to three biotypes. Biotype I (4 isolates) included single entA possessors, whereas biotype II (5 isolates) and biotype III (2 isolates) were m-Ent+ variants profiling entA-entB-entP and entA-entB genes, respectively. Biotype II displayed the strongest antilisterial activity in vitro. Surprisingly, 85.7% (6/7) of the m-Ent+ E. faecium were selectively isolated from Baird-Parker agar, reflecting their natural resistance to 0.01% tellurite contained in the egg yolk supplement. No cytolysin-positive E. faecalis or other Ent+ Enterococcus spp. were isolated. In conclusion, commercially thermized Greek milk is a natural pool or 'reservoir' of antagonistic Ent+ or m-Ent+ E. faecium strains that can be easily detected and recovered by applying this PCR-based approach to naturally fermented milks or cheese products.
Collapse
Affiliation(s)
- Elpiniki Vandera
- Hellenic Agricultural Organization 'DIMITRA', General Directorate of Agricultural Research, Dairy Research Institute, Katsikas, 45221 Ioannina, Greece; University of Ioannina, Department of Chemistry, Laboratory of Biochemistry, 45100 Ioannina, Greece
| | - Georgia Tsirka
- Hellenic Agricultural Organization 'DIMITRA', General Directorate of Agricultural Research, Dairy Research Institute, Katsikas, 45221 Ioannina, Greece; University of Ioannina, Department of Chemistry, Laboratory of Biochemistry, 45100 Ioannina, Greece
| | - Athanasia Kakouri
- Hellenic Agricultural Organization 'DIMITRA', General Directorate of Agricultural Research, Dairy Research Institute, Katsikas, 45221 Ioannina, Greece
| | - Anna-Irini Koukkou
- University of Ioannina, Department of Chemistry, Laboratory of Biochemistry, 45100 Ioannina, Greece
| | - John Samelis
- Hellenic Agricultural Organization 'DIMITRA', General Directorate of Agricultural Research, Dairy Research Institute, Katsikas, 45221 Ioannina, Greece.
| |
Collapse
|
48
|
De Filippis F, Parente E, Ercolini D. Recent Past, Present, and Future of the Food Microbiome. Annu Rev Food Sci Technol 2018; 9:589-608. [DOI: 10.1146/annurev-food-030117-012312] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, 80131 Naples, Italy
| | - Eugenio Parente
- Department of Science, University of Basilicata, 85100 Potenza, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, 80131 Naples, Italy
| |
Collapse
|
49
|
Lima SF, Bicalho MLDS, Bicalho RC. Evaluation of milk sample fractions for characterization of milk microbiota from healthy and clinical mastitis cows. PLoS One 2018; 13:e0193671. [PMID: 29561873 PMCID: PMC5862444 DOI: 10.1371/journal.pone.0193671] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/15/2018] [Indexed: 12/02/2022] Open
Abstract
Amplicon sequencing technique has been increasingly applied to the clinical setting as a sensitive diagnostic tool. Therefore, it is of great importance to develop a DNA extraction method that accurate isolates DNA from complex host-associated microbiota. Given the multifactorial etiology of clinical mastitis and the diversified lifestyle of bacterial species harboring in milk, here four distinct milk sample fractions: raw whole milk, milk fat, casein-pellet, and casein-pellet + fat from healthy cows and cows with clinical mastitis, were subjected to bead-beating DNA extraction, followed by high-throughput sequencing. We aimed to identify the best approach for characterization of the milk microbiota and detection of mastitis pathogens (Klebsiella spp., Streptococcus spp. and Escherichia coli). DNA from each milk fraction tested was extracted by two commercial kits, which include physical, mechanical and chemical lysis; in total 280 DNA samples from 35 cows were analyzed. Milk-health-status were categorized into four groups (healthy group; E. coli-mastitis group; Klebsiella spp.-mastitis group; and Streptococcus spp.–mastitis group). Bacterial phyla and families were described for each milk-health-status group across milk sample fractions and DNA extraction kits. For the mastitis groups the relative abundance of f__Enterobacteriaceae and f__Streptococcaceae were compared to determine the efficacy of procedures in detecting the mastitis pathogens. The four milk fractions used allowed efficiently and uniformly detection of the causative agent of mastitis. Only 27% of the families detected in healthy milk were shared among the samples extracted from all fractions of milk samples; followed by 3, 4, and 12% for the samples from E. coli-mastitis, Klebsiella spp.-mastitis and Streptococcus spp-mastitis, respectively. However, the shared families comprised a mean relative abundance greater than 85%, regardless of milk-health-status, milk fraction and DNA isolation method. Taxonomic data at the family level showed that sequences from mastitis milk samples cultured positive for E. coli and Klebsiella spp. were predominantly affiliated with f__Enterobacteriaceae, while for Streptococcus spp. were dominated by f__Streptococcacea, followed by f__Pseudomonadaceae and f__Enterococcaceae. Microbial community analysis revealed that most of the microbial community composition corresponded to milk bacterial species irrespective of the DNA isolation method and milk fraction evaluated.
Collapse
Affiliation(s)
- Svetlana Ferreira Lima
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York, United States of America
| | - Marcela Lucas de Souza Bicalho
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York, United States of America
| | - Rodrigo Carvalho Bicalho
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York, United States of America
- * E-mail:
| |
Collapse
|
50
|
Aura AM, D'Agata R, Spoto G. Ultrasensitive Detection of Staphylococcus aureus
and Listeria monocytogenes
Genomic DNA by Nanoparticle-Enhanced Surface Plasmon Resonance Imaging. ChemistrySelect 2017. [DOI: 10.1002/slct.201700779] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Angela Margherita Aura
- Dipartimento di Scienze Chimiche; Università di Catania; Viale Andrea Doria 6, I- 95125 Catania Italy
| | - Roberta D'Agata
- Consorzio Interuniversitario “Istituto Nazionale Biostrutture e Biosistemi”, c/o Dipartimento di Scienze Chimiche; Università di Catania; Viale Andrea Doria 6, I- 95125 Catania Italy
| | - Giuseppe Spoto
- Dipartimento di Scienze Chimiche; Università di Catania; Viale Andrea Doria 6, I- 95125 Catania Italy
- Consorzio Interuniversitario “Istituto Nazionale Biostrutture e Biosistemi”, c/o Dipartimento di Scienze Chimiche; Università di Catania; Viale Andrea Doria 6, I- 95125 Catania Italy
| |
Collapse
|